Starting phenix.real_space_refine on Tue Mar 3 13:34:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws7_32749/03_2026/7ws7_32749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws7_32749/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ws7_32749/03_2026/7ws7_32749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws7_32749/03_2026/7ws7_32749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ws7_32749/03_2026/7ws7_32749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws7_32749/03_2026/7ws7_32749.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.32, per 1000 atoms: 0.25 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: 0.42 Conformation dependent library (CDL) restraints added in 314.7 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: 0.21 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: 0.74 Time building geometry restraints manager: 0.59 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 - 21.97: 2954 21.97 - 43.94: 185 43.94 - 65.91: 15 65.91 - 87.88: 13 87.88 - 109.85: 4 Dihedral angle restraints: 3171 sinusoidal: 1236 harmonic: 1935 Sorted by residual: dihedral pdb=" C1 NAG O 2 " pdb=" C2 NAG O 2 " pdb=" C3 NAG O 2 " pdb=" O3 NAG O 2 " ideal model delta sinusoidal sigma weight residual -175.09 -65.24 -109.85 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C1 NAG O 2 " pdb=" C2 NAG O 2 " pdb=" C3 NAG O 2 " pdb=" C4 NAG O 2 " ideal model delta sinusoidal sigma weight residual -52.39 56.91 -109.30 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" N2 NAG O 2 " pdb=" C2 NAG O 2 " pdb=" C3 NAG O 2 " pdb=" O3 NAG O 2 " ideal model delta sinusoidal sigma weight residual 62.25 170.61 -108.36 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 3168 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: 9.510 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.580 Find NCS groups from input model: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 14.978 109.847 1922 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 covalent geometry : bond 0.00487 ( 5338) covalent geometry : angle 0.71210 ( 7253) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.55691 ( 14) hydrogen bonds : bond 0.27495 ( 142) hydrogen bonds : angle 10.35783 ( 384) link_BETA1-4 : bond 0.00530 ( 1) link_BETA1-4 : angle 4.55325 ( 3) link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 17.31197 ( 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 : 0.199 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1032 time to fit residues: 18.0568 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 : 0.241 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3273 r_free = 0.3273 target = 0.085425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073252 restraints weight = 12013.341| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.84 r_work: 0.2946 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5347 Z= 0.150 Angle : 0.653 7.573 7273 Z= 0.334 Chirality : 0.047 0.340 786 Planarity : 0.004 0.034 937 Dihedral : 9.011 81.167 779 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.89 % Allowed : 11.70 % Favored : 87.41 % 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: -1.51 (0.32), residues: 661 helix: -3.74 (0.76), residues: 27 sheet: -0.26 (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 0.013 0.001 TYR F 49 PHE 0.012 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 covalent geometry : bond 0.00343 ( 5338) covalent geometry : angle 0.63912 ( 7253) SS BOND : bond 0.00451 ( 7) SS BOND : angle 0.98610 ( 14) hydrogen bonds : bond 0.04883 ( 142) hydrogen bonds : angle 7.07629 ( 384) link_BETA1-4 : bond 0.00911 ( 1) link_BETA1-4 : angle 4.42350 ( 3) link_NAG-ASN : bond 0.01473 ( 1) link_NAG-ASN : angle 4.84947 ( 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 130 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8820 (t0) cc_final: 0.8263 (t0) REVERT: F 81 GLU cc_start: 0.8505 (pm20) cc_final: 0.8080 (pm20) REVERT: G 99 ASP cc_start: 0.8704 (t70) cc_final: 0.8405 (t70) REVERT: J 101 GLN cc_start: 0.6445 (pp30) cc_final: 0.6030 (pp30) REVERT: K 73 ASP cc_start: 0.8401 (t0) cc_final: 0.8173 (t0) outliers start: 5 outliers final: 4 residues processed: 128 average time/residue: 0.0835 time to fit residues: 13.4708 Evaluate side-chains 121 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.072193 restraints weight = 12032.360| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.78 r_work: 0.2931 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1877 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= 0.153 Angle : 0.616 9.064 7273 Z= 0.308 Chirality : 0.046 0.314 786 Planarity : 0.004 0.034 937 Dihedral : 6.913 52.461 779 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.60 % Allowed : 13.48 % Favored : 84.93 % 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: -1.58 (0.32), residues: 661 helix: -3.61 (0.81), residues: 27 sheet: -0.32 (0.30), residues: 293 loop : -1.47 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 16 TYR 0.012 0.001 TYR B 495 PHE 0.011 0.001 PHE B 377 TRP 0.009 0.001 TRP G 47 HIS 0.001 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5338) covalent geometry : angle 0.60201 ( 7253) SS BOND : bond 0.00432 ( 7) SS BOND : angle 0.77632 ( 14) hydrogen bonds : bond 0.04195 ( 142) hydrogen bonds : angle 6.22056 ( 384) link_BETA1-4 : bond 0.01357 ( 1) link_BETA1-4 : angle 4.34121 ( 3) link_NAG-ASN : bond 0.01066 ( 1) link_NAG-ASN : angle 4.64135 ( 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 133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8790 (t0) cc_final: 0.8415 (t0) REVERT: F 77 SER cc_start: 0.8489 (m) cc_final: 0.8022 (p) REVERT: F 81 GLU cc_start: 0.8593 (pm20) cc_final: 0.8193 (pm20) REVERT: F 82 ASP cc_start: 0.8334 (m-30) cc_final: 0.8114 (m-30) REVERT: G 99 ASP cc_start: 0.8702 (t70) cc_final: 0.8414 (t70) REVERT: K 73 ASP cc_start: 0.8475 (t0) cc_final: 0.8068 (t0) outliers start: 9 outliers final: 5 residues processed: 129 average time/residue: 0.0859 time to fit residues: 13.7671 Evaluate side-chains 120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3237 r_free = 0.3237 target = 0.083510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.071183 restraints weight = 12100.641| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.84 r_work: 0.2908 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5347 Z= 0.181 Angle : 0.624 8.431 7273 Z= 0.312 Chirality : 0.046 0.300 786 Planarity : 0.004 0.036 937 Dihedral : 6.075 45.865 779 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.13 % Allowed : 16.67 % Favored : 81.21 % 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: -1.53 (0.32), residues: 661 helix: -3.55 (0.83), residues: 27 sheet: -0.29 (0.32), residues: 275 loop : -1.39 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 16 TYR 0.013 0.001 TYR B 495 PHE 0.012 0.001 PHE B 392 TRP 0.009 0.001 TRP G 47 HIS 0.002 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 5338) covalent geometry : angle 0.60999 ( 7253) SS BOND : bond 0.00459 ( 7) SS BOND : angle 0.80835 ( 14) hydrogen bonds : bond 0.04004 ( 142) hydrogen bonds : angle 5.90445 ( 384) link_BETA1-4 : bond 0.01245 ( 1) link_BETA1-4 : angle 4.62112 ( 3) link_NAG-ASN : bond 0.00847 ( 1) link_NAG-ASN : angle 4.34589 ( 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 134 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8933 (t0) cc_final: 0.8536 (t0) REVERT: B 441 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9444 (mp) REVERT: B 465 GLU cc_start: 0.7965 (pm20) cc_final: 0.7591 (pm20) REVERT: F 77 SER cc_start: 0.8509 (m) cc_final: 0.8056 (p) REVERT: F 81 GLU cc_start: 0.8621 (pm20) cc_final: 0.8234 (pm20) REVERT: F 82 ASP cc_start: 0.8341 (m-30) cc_final: 0.8110 (m-30) REVERT: G 99 ASP cc_start: 0.8741 (t70) cc_final: 0.8395 (t70) REVERT: K 19 ARG cc_start: 0.8822 (ttt-90) cc_final: 0.8614 (ttt-90) REVERT: K 73 ASP cc_start: 0.8532 (t0) cc_final: 0.8080 (t0) outliers start: 12 outliers final: 8 residues processed: 130 average time/residue: 0.0849 time to fit residues: 13.7483 Evaluate side-chains 128 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 433 VAL 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 Chi-restraints excluded: chain K residue 122 SER 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: 0.6980 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3231 r_free = 0.3231 target = 0.083211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.070873 restraints weight = 12341.257| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.86 r_work: 0.2902 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5347 Z= 0.175 Angle : 0.628 7.678 7273 Z= 0.314 Chirality : 0.045 0.286 786 Planarity : 0.004 0.036 937 Dihedral : 5.726 41.495 779 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.19 % Allowed : 17.38 % Favored : 79.43 % 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: -1.43 (0.32), residues: 661 helix: -3.54 (0.82), residues: 27 sheet: -0.23 (0.30), residues: 299 loop : -1.37 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 87 TYR 0.013 0.001 TYR B 495 PHE 0.027 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 covalent geometry : bond 0.00409 ( 5338) covalent geometry : angle 0.61448 ( 7253) SS BOND : bond 0.00356 ( 7) SS BOND : angle 0.83348 ( 14) hydrogen bonds : bond 0.03849 ( 142) hydrogen bonds : angle 5.70375 ( 384) link_BETA1-4 : bond 0.00940 ( 1) link_BETA1-4 : angle 4.78136 ( 3) link_NAG-ASN : bond 0.00744 ( 1) link_NAG-ASN : angle 4.05674 ( 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 138 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8927 (t0) cc_final: 0.8538 (t0) REVERT: B 465 GLU cc_start: 0.8001 (pm20) cc_final: 0.7491 (pm20) REVERT: B 516 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: F 77 SER cc_start: 0.8487 (m) cc_final: 0.8056 (p) REVERT: F 81 GLU cc_start: 0.8616 (pm20) cc_final: 0.8231 (pm20) REVERT: F 82 ASP cc_start: 0.8381 (m-30) cc_final: 0.8150 (m-30) REVERT: G 99 ASP cc_start: 0.8743 (t70) cc_final: 0.8398 (t70) REVERT: K 73 ASP cc_start: 0.8543 (t0) cc_final: 0.8070 (t0) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.0967 time to fit residues: 15.6753 Evaluate side-chains 131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 73 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 49 SER Chi-restraints excluded: chain K residue 82 GLN 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: 0.2980 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3233 r_free = 0.3233 target = 0.083382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.070906 restraints weight = 12323.159| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.92 r_work: 0.2904 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5347 Z= 0.163 Angle : 0.627 8.226 7273 Z= 0.311 Chirality : 0.045 0.276 786 Planarity : 0.004 0.036 937 Dihedral : 5.477 37.377 779 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.72 % Allowed : 17.38 % 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: -1.41 (0.32), residues: 661 helix: -3.51 (0.82), residues: 27 sheet: -0.24 (0.30), residues: 299 loop : -1.34 (0.32), residues: 335 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 0.014 0.001 PHE B 392 TRP 0.008 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 5338) covalent geometry : angle 0.61442 ( 7253) SS BOND : bond 0.00415 ( 7) SS BOND : angle 0.71242 ( 14) hydrogen bonds : bond 0.03727 ( 142) hydrogen bonds : angle 5.53631 ( 384) link_BETA1-4 : bond 0.01022 ( 1) link_BETA1-4 : angle 4.79177 ( 3) link_NAG-ASN : bond 0.00692 ( 1) link_NAG-ASN : angle 3.83100 ( 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 139 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8855 (t0) cc_final: 0.8369 (t0) REVERT: B 465 GLU cc_start: 0.7917 (pm20) cc_final: 0.7429 (pm20) REVERT: B 516 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: F 77 SER cc_start: 0.8505 (m) cc_final: 0.8056 (p) REVERT: F 81 GLU cc_start: 0.8613 (pm20) cc_final: 0.8201 (pm20) REVERT: F 82 ASP cc_start: 0.8347 (m-30) cc_final: 0.8104 (m-30) REVERT: G 99 ASP cc_start: 0.8730 (t70) cc_final: 0.8389 (t70) REVERT: K 73 ASP cc_start: 0.8557 (t0) cc_final: 0.8010 (t0) outliers start: 21 outliers final: 14 residues processed: 130 average time/residue: 0.0857 time to fit residues: 13.8818 Evaluate side-chains 129 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 516 GLU 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 12 VAL 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 Chi-restraints excluded: chain K residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3252 r_free = 0.3252 target = 0.084354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.071870 restraints weight = 12235.707| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.91 r_work: 0.2923 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2420 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= 0.130 Angle : 0.601 7.483 7273 Z= 0.298 Chirality : 0.045 0.264 786 Planarity : 0.004 0.035 937 Dihedral : 5.103 32.572 779 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.19 % Allowed : 17.73 % 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: -1.37 (0.32), residues: 661 helix: -3.24 (0.74), residues: 33 sheet: -0.16 (0.31), residues: 287 loop : -1.30 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 87 TYR 0.009 0.001 TYR B 495 PHE 0.014 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 covalent geometry : bond 0.00305 ( 5338) covalent geometry : angle 0.58938 ( 7253) SS BOND : bond 0.00361 ( 7) SS BOND : angle 0.62700 ( 14) hydrogen bonds : bond 0.03443 ( 142) hydrogen bonds : angle 5.28773 ( 384) link_BETA1-4 : bond 0.00949 ( 1) link_BETA1-4 : angle 4.71161 ( 3) link_NAG-ASN : bond 0.00695 ( 1) link_NAG-ASN : angle 3.59463 ( 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 136 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8808 (t0) cc_final: 0.8383 (t0) REVERT: B 465 GLU cc_start: 0.7885 (pm20) cc_final: 0.7411 (pm20) REVERT: B 516 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: F 77 SER cc_start: 0.8480 (m) cc_final: 0.8037 (p) REVERT: F 81 GLU cc_start: 0.8583 (pm20) cc_final: 0.8174 (pm20) REVERT: F 82 ASP cc_start: 0.8323 (m-30) cc_final: 0.8082 (m-30) REVERT: G 99 ASP cc_start: 0.8707 (t70) cc_final: 0.8393 (t70) REVERT: K 46 GLU cc_start: 0.8365 (tt0) cc_final: 0.8113 (mt-10) REVERT: K 73 ASP cc_start: 0.8533 (t0) cc_final: 0.8008 (t0) outliers start: 18 outliers final: 15 residues processed: 127 average time/residue: 0.0858 time to fit residues: 13.5164 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 : 0.191 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 12 VAL 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 J residue 98 THR Chi-restraints excluded: chain K residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3247 r_free = 0.3247 target = 0.084147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.071790 restraints weight = 12052.254| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.89 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: 0.8511 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5347 Z= 0.137 Angle : 0.602 6.915 7273 Z= 0.299 Chirality : 0.044 0.259 786 Planarity : 0.004 0.035 937 Dihedral : 4.901 28.535 779 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.01 % Allowed : 18.26 % Favored : 78.72 % 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: -3.27 (0.73), residues: 33 sheet: -0.11 (0.30), residues: 297 loop : -1.22 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 87 TYR 0.010 0.001 TYR B 495 PHE 0.015 0.001 PHE B 392 TRP 0.007 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5338) covalent geometry : angle 0.59094 ( 7253) SS BOND : bond 0.00358 ( 7) SS BOND : angle 0.61335 ( 14) hydrogen bonds : bond 0.03397 ( 142) hydrogen bonds : angle 5.17444 ( 384) link_BETA1-4 : bond 0.00798 ( 1) link_BETA1-4 : angle 4.62643 ( 3) link_NAG-ASN : bond 0.00647 ( 1) link_NAG-ASN : angle 3.47911 ( 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 134 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8794 (t0) cc_final: 0.8396 (t0) REVERT: B 465 GLU cc_start: 0.7876 (pm20) cc_final: 0.7395 (pm20) REVERT: B 516 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: F 77 SER cc_start: 0.8472 (m) cc_final: 0.8031 (p) REVERT: F 81 GLU cc_start: 0.8586 (pm20) cc_final: 0.8176 (pm20) REVERT: F 82 ASP cc_start: 0.8343 (m-30) cc_final: 0.8094 (m-30) REVERT: G 99 ASP cc_start: 0.8722 (t70) cc_final: 0.8403 (t70) REVERT: K 73 ASP cc_start: 0.8526 (t0) cc_final: 0.8013 (t0) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 0.0855 time to fit residues: 13.7757 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 : 0.220 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 12 VAL 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: 0.5980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3273 r_free = 0.3273 target = 0.085462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073035 restraints weight = 12109.973| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.91 r_work: 0.2941 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2594 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= 0.117 Angle : 0.600 6.602 7273 Z= 0.299 Chirality : 0.044 0.249 786 Planarity : 0.003 0.034 937 Dihedral : 4.659 24.295 779 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.19 % Allowed : 18.26 % Favored : 78.55 % 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: -1.24 (0.32), residues: 661 helix: -3.26 (0.73), residues: 33 sheet: 0.09 (0.32), residues: 269 loop : -1.30 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 16 TYR 0.008 0.001 TYR G 95 PHE 0.014 0.001 PHE B 392 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 5338) covalent geometry : angle 0.58972 ( 7253) SS BOND : bond 0.00305 ( 7) SS BOND : angle 0.60281 ( 14) hydrogen bonds : bond 0.03188 ( 142) hydrogen bonds : angle 5.00571 ( 384) link_BETA1-4 : bond 0.00759 ( 1) link_BETA1-4 : angle 4.40771 ( 3) link_NAG-ASN : bond 0.00686 ( 1) link_NAG-ASN : angle 3.29281 ( 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 133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8787 (t0) cc_final: 0.8411 (t0) REVERT: B 465 GLU cc_start: 0.7818 (pm20) cc_final: 0.7344 (pm20) REVERT: B 516 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: F 77 SER cc_start: 0.8397 (m) cc_final: 0.7943 (p) REVERT: F 81 GLU cc_start: 0.8560 (pm20) cc_final: 0.8157 (pm20) REVERT: F 82 ASP cc_start: 0.8297 (m-30) cc_final: 0.8054 (m-30) REVERT: G 99 ASP cc_start: 0.8693 (t70) cc_final: 0.8395 (t70) REVERT: K 73 ASP cc_start: 0.8466 (t0) cc_final: 0.8019 (t0) outliers start: 18 outliers final: 17 residues processed: 126 average time/residue: 0.0861 time to fit residues: 13.5990 Evaluate side-chains 132 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 516 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 12 VAL 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 J residue 98 THR 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 27 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3259 r_free = 0.3259 target = 0.084621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072278 restraints weight = 12082.333| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.91 r_work: 0.2932 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2691 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= 0.133 Angle : 0.609 6.403 7273 Z= 0.305 Chirality : 0.044 0.246 786 Planarity : 0.004 0.035 937 Dihedral : 4.635 21.611 779 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.55 % Allowed : 18.26 % Favored : 78.19 % 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: -3.29 (0.72), residues: 33 sheet: -0.14 (0.31), residues: 291 loop : -1.18 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 16 TYR 0.010 0.001 TYR B 495 PHE 0.013 0.001 PHE B 392 TRP 0.007 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5338) covalent geometry : angle 0.59936 ( 7253) SS BOND : bond 0.00331 ( 7) SS BOND : angle 0.66991 ( 14) hydrogen bonds : bond 0.03259 ( 142) hydrogen bonds : angle 5.00158 ( 384) link_BETA1-4 : bond 0.00710 ( 1) link_BETA1-4 : angle 4.27637 ( 3) link_NAG-ASN : bond 0.00612 ( 1) link_NAG-ASN : angle 3.23439 ( 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 132 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8790 (t0) cc_final: 0.8400 (t0) REVERT: B 465 GLU cc_start: 0.7831 (pm20) cc_final: 0.7362 (pm20) REVERT: B 516 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: F 77 SER cc_start: 0.8416 (m) cc_final: 0.7956 (p) REVERT: F 81 GLU cc_start: 0.8575 (pm20) cc_final: 0.8166 (pm20) REVERT: F 82 ASP cc_start: 0.8280 (m-30) cc_final: 0.8026 (m-30) REVERT: G 99 ASP cc_start: 0.8725 (t70) cc_final: 0.8423 (t70) REVERT: K 73 ASP cc_start: 0.8490 (t0) cc_final: 0.8037 (t0) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.0889 time to fit residues: 13.7289 Evaluate side-chains 131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 516 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3272 r_free = 0.3272 target = 0.085384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073049 restraints weight = 12231.446| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.93 r_work: 0.2944 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5347 Z= 0.119 Angle : 0.595 6.156 7273 Z= 0.298 Chirality : 0.044 0.238 786 Planarity : 0.003 0.034 937 Dihedral : 4.502 18.513 779 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.84 % Allowed : 18.97 % Favored : 78.19 % 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: -1.26 (0.32), residues: 661 helix: -3.30 (0.71), residues: 33 sheet: 0.02 (0.31), residues: 273 loop : -1.29 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 16 TYR 0.010 0.001 TYR B 369 PHE 0.012 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 covalent geometry : bond 0.00280 ( 5338) covalent geometry : angle 0.58653 ( 7253) SS BOND : bond 0.00310 ( 7) SS BOND : angle 0.59065 ( 14) hydrogen bonds : bond 0.03117 ( 142) hydrogen bonds : angle 4.93412 ( 384) link_BETA1-4 : bond 0.00703 ( 1) link_BETA1-4 : angle 4.03723 ( 3) link_NAG-ASN : bond 0.00618 ( 1) link_NAG-ASN : angle 3.07240 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.79 seconds wall clock time: 27 minutes 51.51 seconds (1671.51 seconds total)