Starting phenix.real_space_refine on Thu Jul 2 01:25:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws7_32749/07_2026/7ws7_32749.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.026 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 22 5.16 5 C 3294 2.51 5 N 869 2.21 5 O 1024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5209 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 192} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "O" 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 chiralities: 2 Time building chain proxies: 0.99, per 1000 atoms: 0.19 Number of scatterers: 5209 At special positions: 0 Unit cell: (77.08, 100.04, 120.54, 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 22 16.00 O 1024 8.00 N 869 7.00 C 3294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " 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 O 1 " - " NAG O 2 " NAG-ASN " NAG O 1 " - " ASN B 343 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 148.8 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 8.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.619A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.711A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.733A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.672A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.581A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.603A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.908A pdb=" N ASP K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.877A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.786A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.494A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.761A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.860A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.701A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 98 through 99 removed outlier: 6.424A pdb=" N LYS G 98 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.804A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.164A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.926A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR J 98 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR K 112 " --> pdb=" O LYS K 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR K 94 " --> pdb=" O THR K 117 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 384 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: 0.73 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1672 1.34 - 1.46: 1353 1.46 - 1.58: 2285 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 5338 Sorted by residual: bond pdb=" N ASP B 442 " pdb=" CA ASP B 442 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.10e-02 8.26e+03 1.06e+01 bond pdb=" N VAL B 445 " pdb=" CA VAL B 445 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.36e+00 bond pdb=" N VAL B 382 " pdb=" CA VAL B 382 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" N PHE B 392 " pdb=" CA PHE B 392 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.09e-02 8.42e+03 7.67e+00 bond pdb=" N GLU K 103 " pdb=" CA GLU K 103 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.64e+00 ... (remaining 5333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 6605 1.15 - 2.29: 495 2.29 - 3.44: 127 3.44 - 4.58: 18 4.58 - 5.73: 8 Bond angle restraints: 7253 Sorted by residual: angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.53 110.01 3.52 9.80e-01 1.04e+00 1.29e+01 angle pdb=" N LYS B 386 " pdb=" CA LYS B 386 " pdb=" C LYS B 386 " ideal model delta sigma weight residual 112.92 108.82 4.10 1.23e+00 6.61e-01 1.11e+01 angle pdb=" CA VAL B 445 " pdb=" C VAL B 445 " pdb=" O VAL B 445 " ideal model delta sigma weight residual 120.95 117.63 3.32 1.04e+00 9.25e-01 1.02e+01 angle pdb=" C ARG B 509 " pdb=" CA ARG B 509 " pdb=" CB ARG B 509 " ideal model delta sigma weight residual 109.72 104.73 4.99 1.66e+00 3.63e-01 9.04e+00 angle pdb=" CA SER F 67 " pdb=" C SER F 67 " pdb=" O SER F 67 " ideal model delta sigma weight residual 121.45 118.28 3.17 1.07e+00 8.73e-01 8.76e+00 ... (remaining 7248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 2820 16.46 - 32.92: 238 32.92 - 49.38: 56 49.38 - 65.84: 8 65.84 - 82.30: 7 Dihedral angle restraints: 3129 sinusoidal: 1194 harmonic: 1935 Sorted by residual: dihedral pdb=" CA PRO F 95 " pdb=" C PRO F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual -180.00 -163.87 -16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA PHE B 464 " pdb=" C PHE B 464 " pdb=" N GLU B 465 " pdb=" CA GLU B 465 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.65e+00 dihedral pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " pdb=" OE1 GLU B 471 " ideal model delta sinusoidal sigma weight residual 0.00 -82.30 82.30 1 3.00e+01 1.11e-03 9.24e+00 ... (remaining 3126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 690 0.078 - 0.155: 89 0.155 - 0.232: 6 0.232 - 0.310: 0 0.310 - 0.387: 1 Chirality restraints: 786 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ARG B 509 " pdb=" N ARG B 509 " pdb=" C ARG B 509 " pdb=" CB ARG B 509 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL B 382 " pdb=" CA VAL B 382 " pdb=" CG1 VAL B 382 " pdb=" CG2 VAL B 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 783 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.095 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" CG ASN B 343 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.243 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F 79 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.87e+00 pdb=" N PRO F 80 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 387 " -0.010 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C LEU B 387 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 387 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 388 " -0.013 2.00e-02 2.50e+03 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 14 2.44 - 3.05: 3147 3.05 - 3.67: 7333 3.67 - 4.28: 10603 4.28 - 4.90: 18849 Nonbonded interactions: 39946 Sorted by model distance: nonbonded pdb=" OD1 ASN B 343 " pdb=" O7 NAG O 1 " model vdw 1.820 3.040 nonbonded pdb=" OH TYR F 97 " pdb=" O ILE G 104 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASP B 420 " pdb=" ND2 ASN B 460 " model vdw 2.185 3.120 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.304 3.120 nonbonded pdb=" NH2 ARG K 67 " pdb=" OD2 ASP K 90 " model vdw 2.316 3.120 ... (remaining 39941 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 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' } 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: 9.560 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.005 0.064 5347 Z= 0.305 Angle : 0.799 23.368 7273 Z= 0.449 Chirality : 0.050 0.387 786 Planarity : 0.004 0.070 937 Dihedral : 13.344 82.301 1880 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.32), residues: 661 helix: -3.72 (0.75), residues: 27 sheet: -0.67 (0.32), residues: 280 loop : -1.37 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 16 TYR 0.019 0.001 TYR F 49 PHE 0.013 0.001 PHE J 83 TRP 0.007 0.001 TRP K 47 HIS 0.001 0.000 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.30 ( 5338) covalent geometry : angle 0.71210 / 0.43 ( 7253) SS BOND : bond 0.00281 / 0.15 ( 7) SS BOND : angle 0.55691 / 0.28 ( 14) hydrogen bonds : bond 0.27495 / 17.49 ( 142) hydrogen bonds : angle 10.35783 / 7.33 ( 384) link_BETA1-4 : bond 0.00530 / 0.28 ( 1) link_BETA1-4 : angle 4.55325 / 2.30 ( 3) link_NAG-ASN : bond 0.00169 / 0.09 ( 1) link_NAG-ASN : angle 17.31197 / 8.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.218 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0871 time to fit residues: 15.4171 Evaluate side-chains 118 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 ASN F 6 GLN F 34 ASN K 77 ASN K 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073470 restraints weight = 12000.224| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.81 r_work: 0.2951 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5347 Z= 0.141 Angle : 0.633 7.957 7273 Z= 0.324 Chirality : 0.047 0.358 786 Planarity : 0.004 0.037 937 Dihedral : 4.513 24.454 737 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.06 % Allowed : 11.88 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.32), residues: 661 helix: -3.74 (0.76), residues: 27 sheet: -0.27 (0.32), residues: 279 loop : -1.38 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.014 0.001 TYR F 49 PHE 0.015 0.001 PHE B 377 TRP 0.010 0.001 TRP G 47 HIS 0.001 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5338) covalent geometry : angle 0.62064 / 0.32 ( 7253) SS BOND : bond 0.00421 / 0.21 ( 7) SS BOND : angle 0.85940 / 0.41 ( 14) hydrogen bonds : bond 0.04631 / 2.89 ( 142) hydrogen bonds : angle 6.94728 / 4.93 ( 384) link_BETA1-4 : bond 0.00802 / 0.42 ( 1) link_BETA1-4 : angle 3.75530 / 1.89 ( 3) link_NAG-ASN : bond 0.01747 / 0.92 ( 1) link_NAG-ASN : angle 4.90394 / 2.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8816 (t0) cc_final: 0.8270 (t0) REVERT: F 81 GLU cc_start: 0.8533 (pm20) cc_final: 0.8084 (pm20) REVERT: G 99 ASP cc_start: 0.8685 (t70) cc_final: 0.8379 (t70) REVERT: K 73 ASP cc_start: 0.8408 (t0) cc_final: 0.8110 (t0) outliers start: 6 outliers final: 4 residues processed: 128 average time/residue: 0.0781 time to fit residues: 12.5836 Evaluate side-chains 119 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 82 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072205 restraints weight = 11972.609| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.83 r_work: 0.2926 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5347 Z= 0.161 Angle : 0.608 7.487 7273 Z= 0.309 Chirality : 0.045 0.303 786 Planarity : 0.004 0.034 937 Dihedral : 4.573 25.684 737 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.77 % Allowed : 13.83 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.32), residues: 661 helix: -3.60 (0.81), residues: 27 sheet: -0.36 (0.30), residues: 293 loop : -1.46 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 16 TYR 0.012 0.001 TYR B 495 PHE 0.011 0.001 PHE B 377 TRP 0.010 0.001 TRP G 47 HIS 0.001 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 5338) covalent geometry : angle 0.59651 / 0.31 ( 7253) SS BOND : bond 0.00438 / 0.23 ( 7) SS BOND : angle 0.78337 / 0.40 ( 14) hydrogen bonds : bond 0.04215 / 2.62 ( 142) hydrogen bonds : angle 6.20200 / 4.39 ( 384) link_BETA1-4 : bond 0.01219 / 0.64 ( 1) link_BETA1-4 : angle 3.61141 / 1.82 ( 3) link_NAG-ASN : bond 0.01060 / 0.56 ( 1) link_NAG-ASN : angle 4.58176 / 2.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8799 (t0) cc_final: 0.8424 (t0) REVERT: F 77 SER cc_start: 0.8496 (m) cc_final: 0.8029 (p) REVERT: F 81 GLU cc_start: 0.8621 (pm20) cc_final: 0.8239 (pm20) REVERT: F 82 ASP cc_start: 0.8324 (m-30) cc_final: 0.8102 (m-30) REVERT: G 99 ASP cc_start: 0.8697 (t70) cc_final: 0.8338 (t70) REVERT: K 73 ASP cc_start: 0.8522 (t0) cc_final: 0.8132 (t0) outliers start: 10 outliers final: 6 residues processed: 129 average time/residue: 0.0801 time to fit residues: 13.0144 Evaluate side-chains 121 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 82 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.0050 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN K 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073132 restraints weight = 11918.879| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.83 r_work: 0.2946 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5347 Z= 0.118 Angle : 0.587 7.041 7273 Z= 0.294 Chirality : 0.044 0.283 786 Planarity : 0.003 0.033 937 Dihedral : 4.416 22.982 737 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.95 % Allowed : 15.96 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.32), residues: 661 helix: -3.58 (0.81), residues: 27 sheet: -0.11 (0.32), residues: 267 loop : -1.35 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 16 TYR 0.009 0.001 TYR B 495 PHE 0.028 0.001 PHE B 392 TRP 0.008 0.001 TRP K 47 HIS 0.001 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5338) covalent geometry : angle 0.57657 / 0.29 ( 7253) SS BOND : bond 0.00334 / 0.17 ( 7) SS BOND : angle 0.60584 / 0.30 ( 14) hydrogen bonds : bond 0.03702 / 2.30 ( 142) hydrogen bonds : angle 5.75679 / 4.07 ( 384) link_BETA1-4 : bond 0.01143 / 0.60 ( 1) link_BETA1-4 : angle 3.42923 / 1.73 ( 3) link_NAG-ASN : bond 0.01039 / 0.55 ( 1) link_NAG-ASN : angle 4.10199 / 2.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8908 (t0) cc_final: 0.8515 (t0) REVERT: B 441 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9459 (mp) REVERT: B 516 GLU cc_start: 0.7876 (mp0) cc_final: 0.6953 (mp0) REVERT: F 77 SER cc_start: 0.8484 (m) cc_final: 0.8025 (p) REVERT: F 81 GLU cc_start: 0.8602 (pm20) cc_final: 0.8223 (pm20) REVERT: F 82 ASP cc_start: 0.8290 (m-30) cc_final: 0.8080 (m-30) REVERT: G 99 ASP cc_start: 0.8683 (t70) cc_final: 0.8396 (t70) REVERT: K 19 ARG cc_start: 0.8758 (ttt-90) cc_final: 0.8485 (ttt-90) REVERT: K 73 ASP cc_start: 0.8493 (t0) cc_final: 0.8013 (t0) REVERT: K 82 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8122 (tt0) outliers start: 11 outliers final: 6 residues processed: 127 average time/residue: 0.0737 time to fit residues: 11.7099 Evaluate side-chains 122 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 82 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.084090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071648 restraints weight = 12253.651| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.93 r_work: 0.2912 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5347 Z= 0.163 Angle : 0.596 6.500 7273 Z= 0.302 Chirality : 0.045 0.271 786 Planarity : 0.004 0.034 937 Dihedral : 4.486 22.026 737 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.19 % Allowed : 16.49 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.32), residues: 661 helix: -3.50 (0.85), residues: 27 sheet: -0.18 (0.31), residues: 287 loop : -1.36 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 16 TYR 0.012 0.001 TYR B 495 PHE 0.024 0.001 PHE B 392 TRP 0.008 0.001 TRP G 47 HIS 0.002 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 5338) covalent geometry : angle 0.58709 / 0.30 ( 7253) SS BOND : bond 0.00392 / 0.21 ( 7) SS BOND : angle 0.77219 / 0.40 ( 14) hydrogen bonds : bond 0.03742 / 2.33 ( 142) hydrogen bonds : angle 5.54502 / 3.92 ( 384) link_BETA1-4 : bond 0.01116 / 0.59 ( 1) link_BETA1-4 : angle 3.33920 / 1.69 ( 3) link_NAG-ASN : bond 0.00827 / 0.44 ( 1) link_NAG-ASN : angle 3.89229 / 1.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8866 (t0) cc_final: 0.8487 (t0) REVERT: B 516 GLU cc_start: 0.8046 (mp0) cc_final: 0.7091 (mp0) REVERT: F 77 SER cc_start: 0.8487 (m) cc_final: 0.8040 (p) REVERT: F 81 GLU cc_start: 0.8609 (pm20) cc_final: 0.8205 (pm20) REVERT: F 82 ASP cc_start: 0.8330 (m-30) cc_final: 0.8097 (m-30) REVERT: G 99 ASP cc_start: 0.8735 (t70) cc_final: 0.8377 (t70) REVERT: K 19 ARG cc_start: 0.8806 (ttt-90) cc_final: 0.8546 (ttt-90) REVERT: K 73 ASP cc_start: 0.8528 (t0) cc_final: 0.8050 (t0) outliers start: 18 outliers final: 12 residues processed: 129 average time/residue: 0.0800 time to fit residues: 12.9787 Evaluate side-chains 125 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 122 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** 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 = 0.3268 r_free = 0.3268 target = 0.085146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.072550 restraints weight = 12249.354| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.94 r_work: 0.2934 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5347 Z= 0.120 Angle : 0.578 7.982 7273 Z= 0.289 Chirality : 0.044 0.253 786 Planarity : 0.003 0.034 937 Dihedral : 4.320 21.265 737 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.66 % Allowed : 18.26 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.32), residues: 661 helix: -3.20 (0.77), residues: 33 sheet: -0.10 (0.31), residues: 287 loop : -1.27 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 16 TYR 0.009 0.001 TYR K 32 PHE 0.017 0.001 PHE B 392 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 5338) covalent geometry : angle 0.56964 / 0.29 ( 7253) SS BOND : bond 0.00339 / 0.18 ( 7) SS BOND : angle 0.61228 / 0.31 ( 14) hydrogen bonds : bond 0.03380 / 2.11 ( 142) hydrogen bonds : angle 5.23976 / 3.70 ( 384) link_BETA1-4 : bond 0.00987 / 0.52 ( 1) link_BETA1-4 : angle 3.18130 / 1.61 ( 3) link_NAG-ASN : bond 0.00819 / 0.43 ( 1) link_NAG-ASN : angle 3.50815 / 1.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8823 (t0) cc_final: 0.8487 (t0) REVERT: B 516 GLU cc_start: 0.8073 (mp0) cc_final: 0.7107 (mp0) REVERT: F 77 SER cc_start: 0.8470 (m) cc_final: 0.8031 (p) REVERT: F 81 GLU cc_start: 0.8575 (pm20) cc_final: 0.8180 (pm20) REVERT: F 82 ASP cc_start: 0.8290 (m-30) cc_final: 0.8075 (m-30) REVERT: G 99 ASP cc_start: 0.8690 (t70) cc_final: 0.8360 (t70) REVERT: K 46 GLU cc_start: 0.8328 (tt0) cc_final: 0.8110 (mt-10) REVERT: K 73 ASP cc_start: 0.8502 (t0) cc_final: 0.8018 (t0) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.0858 time to fit residues: 13.4257 Evaluate side-chains 122 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.068684 restraints weight = 12442.941| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.93 r_work: 0.2854 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 5347 Z= 0.281 Angle : 0.690 6.671 7273 Z= 0.352 Chirality : 0.047 0.259 786 Planarity : 0.004 0.037 937 Dihedral : 4.942 21.285 737 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.37 % Allowed : 17.73 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.32), residues: 661 helix: -3.53 (0.79), residues: 27 sheet: -0.20 (0.31), residues: 291 loop : -1.40 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 16 TYR 0.017 0.002 TYR B 495 PHE 0.021 0.002 PHE B 392 TRP 0.011 0.001 TRP G 47 HIS 0.002 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.28 ( 5338) covalent geometry : angle 0.68169 / 0.35 ( 7253) SS BOND : bond 0.00584 / 0.31 ( 7) SS BOND : angle 1.05597 / 0.56 ( 14) hydrogen bonds : bond 0.04073 / 2.53 ( 142) hydrogen bonds : angle 5.55008 / 3.91 ( 384) link_BETA1-4 : bond 0.01039 / 0.55 ( 1) link_BETA1-4 : angle 3.38059 / 1.71 ( 3) link_NAG-ASN : bond 0.00395 / 0.21 ( 1) link_NAG-ASN : angle 3.70258 / 1.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8927 (t0) cc_final: 0.8413 (t0) REVERT: F 77 SER cc_start: 0.8545 (m) cc_final: 0.8107 (p) REVERT: F 81 GLU cc_start: 0.8632 (pm20) cc_final: 0.8212 (pm20) REVERT: F 82 ASP cc_start: 0.8469 (m-30) cc_final: 0.8211 (m-30) REVERT: G 99 ASP cc_start: 0.8800 (t70) cc_final: 0.8386 (t70) REVERT: K 73 ASP cc_start: 0.8613 (t0) cc_final: 0.8038 (t0) REVERT: K 77 ASN cc_start: 0.8714 (m110) cc_final: 0.8464 (m110) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 0.0893 time to fit residues: 14.1244 Evaluate side-chains 125 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 122 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071363 restraints weight = 12074.810| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.89 r_work: 0.2908 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5347 Z= 0.135 Angle : 0.611 6.296 7273 Z= 0.308 Chirality : 0.045 0.241 786 Planarity : 0.004 0.035 937 Dihedral : 4.606 20.909 737 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.19 % Allowed : 17.91 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.32), residues: 661 helix: -3.35 (0.72), residues: 33 sheet: -0.23 (0.31), residues: 293 loop : -1.30 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 16 TYR 0.010 0.001 TYR K 32 PHE 0.028 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 5338) covalent geometry : angle 0.60383 / 0.31 ( 7253) SS BOND : bond 0.00371 / 0.20 ( 7) SS BOND : angle 0.68678 / 0.36 ( 14) hydrogen bonds : bond 0.03473 / 2.20 ( 142) hydrogen bonds : angle 5.25411 / 3.71 ( 384) link_BETA1-4 : bond 0.01021 / 0.54 ( 1) link_BETA1-4 : angle 3.10030 / 1.56 ( 3) link_NAG-ASN : bond 0.00693 / 0.36 ( 1) link_NAG-ASN : angle 3.25876 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8829 (t0) cc_final: 0.8485 (t0) REVERT: B 516 GLU cc_start: 0.8159 (mp0) cc_final: 0.7224 (mp0) REVERT: F 77 SER cc_start: 0.8504 (m) cc_final: 0.8055 (p) REVERT: F 81 GLU cc_start: 0.8609 (pm20) cc_final: 0.8197 (pm20) REVERT: F 82 ASP cc_start: 0.8383 (m-30) cc_final: 0.8125 (m-30) REVERT: G 99 ASP cc_start: 0.8722 (t70) cc_final: 0.8374 (t70) REVERT: K 32 TYR cc_start: 0.9054 (m-80) cc_final: 0.8847 (m-80) REVERT: K 46 GLU cc_start: 0.8398 (tt0) cc_final: 0.8138 (mt-10) REVERT: K 73 ASP cc_start: 0.8520 (t0) cc_final: 0.8028 (t0) outliers start: 18 outliers final: 15 residues processed: 134 average time/residue: 0.0828 time to fit residues: 13.7945 Evaluate side-chains 132 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 122 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.072698 restraints weight = 12068.907| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.89 r_work: 0.2943 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5347 Z= 0.107 Angle : 0.588 6.041 7273 Z= 0.296 Chirality : 0.044 0.232 786 Planarity : 0.004 0.034 937 Dihedral : 4.355 20.316 737 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.30 % Allowed : 19.33 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.32), residues: 661 helix: -3.34 (0.74), residues: 33 sheet: 0.05 (0.31), residues: 273 loop : -1.42 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 16 TYR 0.008 0.001 TYR B 451 PHE 0.021 0.001 PHE B 392 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 5338) covalent geometry : angle 0.58288 / 0.30 ( 7253) SS BOND : bond 0.00264 / 0.14 ( 7) SS BOND : angle 0.56120 / 0.28 ( 14) hydrogen bonds : bond 0.03169 / 1.99 ( 142) hydrogen bonds : angle 4.99692 / 3.55 ( 384) link_BETA1-4 : bond 0.01032 / 0.54 ( 1) link_BETA1-4 : angle 2.77477 / 1.41 ( 3) link_NAG-ASN : bond 0.00699 / 0.37 ( 1) link_NAG-ASN : angle 2.99519 / 1.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8792 (t0) cc_final: 0.8404 (t0) REVERT: B 516 GLU cc_start: 0.8140 (mp0) cc_final: 0.7182 (mp0) REVERT: F 77 SER cc_start: 0.8471 (m) cc_final: 0.8033 (p) REVERT: F 81 GLU cc_start: 0.8600 (pm20) cc_final: 0.8195 (pm20) REVERT: F 82 ASP cc_start: 0.8345 (m-30) cc_final: 0.8083 (m-30) REVERT: G 99 ASP cc_start: 0.8691 (t70) cc_final: 0.8362 (t70) REVERT: K 73 ASP cc_start: 0.8455 (t0) cc_final: 0.7986 (t0) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.0826 time to fit residues: 13.1069 Evaluate side-chains 127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 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 = 0.3252 r_free = 0.3252 target = 0.084245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.071937 restraints weight = 12152.498| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.90 r_work: 0.2922 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5347 Z= 0.150 Angle : 0.603 5.740 7273 Z= 0.304 Chirality : 0.045 0.230 786 Planarity : 0.004 0.035 937 Dihedral : 4.438 20.436 737 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.84 % Allowed : 18.79 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.32), residues: 661 helix: -3.40 (0.73), residues: 33 sheet: -0.10 (0.30), residues: 292 loop : -1.30 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 16 TYR 0.014 0.001 TYR J 92 PHE 0.022 0.001 PHE B 392 TRP 0.007 0.001 TRP K 47 HIS 0.003 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 5338) covalent geometry : angle 0.59735 / 0.30 ( 7253) SS BOND : bond 0.00355 / 0.19 ( 7) SS BOND : angle 0.79416 / 0.41 ( 14) hydrogen bonds : bond 0.03256 / 2.02 ( 142) hydrogen bonds : angle 5.00677 / 3.54 ( 384) link_BETA1-4 : bond 0.01132 / 0.60 ( 1) link_BETA1-4 : angle 2.81344 / 1.43 ( 3) link_NAG-ASN : bond 0.00571 / 0.30 ( 1) link_NAG-ASN : angle 2.98912 / 1.49 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8803 (t0) cc_final: 0.8406 (t0) REVERT: B 516 GLU cc_start: 0.8119 (mp0) cc_final: 0.7171 (mp0) REVERT: F 77 SER cc_start: 0.8469 (m) cc_final: 0.8030 (p) REVERT: F 81 GLU cc_start: 0.8620 (pm20) cc_final: 0.8218 (pm20) REVERT: F 82 ASP cc_start: 0.8383 (m-30) cc_final: 0.8112 (m-30) REVERT: G 99 ASP cc_start: 0.8722 (t70) cc_final: 0.8400 (t70) REVERT: K 73 ASP cc_start: 0.8493 (t0) cc_final: 0.7995 (t0) outliers start: 16 outliers final: 16 residues processed: 124 average time/residue: 0.0905 time to fit residues: 14.1081 Evaluate side-chains 128 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 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 = 0.3239 r_free = 0.3239 target = 0.083605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071302 restraints weight = 12305.058| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.92 r_work: 0.2912 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5347 Z= 0.154 Angle : 0.611 5.796 7273 Z= 0.308 Chirality : 0.045 0.223 786 Planarity : 0.004 0.035 937 Dihedral : 4.514 20.460 737 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.37 % Allowed : 18.26 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.32), residues: 661 helix: -3.48 (0.71), residues: 33 sheet: -0.08 (0.30), residues: 302 loop : -1.26 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 16 TYR 0.013 0.001 TYR J 92 PHE 0.023 0.001 PHE B 392 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 5338) covalent geometry : angle 0.60519 / 0.31 ( 7253) SS BOND : bond 0.00361 / 0.19 ( 7) SS BOND : angle 0.82229 / 0.43 ( 14) hydrogen bonds : bond 0.03292 / 2.04 ( 142) hydrogen bonds : angle 5.06041 / 3.57 ( 384) link_BETA1-4 : bond 0.01031 / 0.54 ( 1) link_BETA1-4 : angle 2.76665 / 1.40 ( 3) link_NAG-ASN : bond 0.00477 / 0.25 ( 1) link_NAG-ASN : angle 2.83691 / 1.40 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1517.73 seconds wall clock time: 26 minutes 45.31 seconds (1605.31 seconds total)