Starting phenix.real_space_refine on Thu Jun 5 05:27:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws7_32749/06_2025/7ws7_32749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws7_32749/06_2025/7ws7_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_32749/06_2025/7ws7_32749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws7_32749/06_2025/7ws7_32749.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws7_32749/06_2025/7ws7_32749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws7_32749/06_2025/7ws7_32749.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.87, per 1000 atoms: 0.93 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: 1.18 Conformation dependent library (CDL) restraints added in 665.6 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: 0.68 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: 1.40 Time building geometry restraints manager: 1.43 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: 9.980 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.32), 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 TRP 0.007 0.001 TRP K 47 HIS 0.001 0.000 HIS G 35 PHE 0.013 0.001 PHE J 83 TYR 0.019 0.001 TYR F 49 ARG 0.007 0.001 ARG G 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 17.31197 ( 3) link_BETA1-4 : bond 0.00530 ( 1) link_BETA1-4 : angle 4.55325 ( 3) hydrogen bonds : bond 0.27495 ( 142) hydrogen bonds : angle 10.35783 ( 384) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.55691 ( 14) covalent geometry : bond 0.00487 ( 5338) covalent geometry : angle 0.71210 ( 7253) *********************** 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 : 0.522 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2223 time to fit residues: 39.2889 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 : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.082554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.070241 restraints weight = 11926.793| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.82 r_work: 0.2886 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5347 Z= 0.249 Angle : 0.710 8.562 7273 Z= 0.359 Chirality : 0.049 0.323 786 Planarity : 0.004 0.039 937 Dihedral : 8.546 73.184 779 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.42 % Allowed : 12.23 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.32), residues: 661 helix: -3.62 (0.82), residues: 27 sheet: -0.52 (0.32), residues: 285 loop : -1.51 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 47 HIS 0.002 0.001 HIS K 35 PHE 0.018 0.002 PHE B 377 TYR 0.017 0.001 TYR B 495 ARG 0.006 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01495 ( 1) link_NAG-ASN : angle 5.33188 ( 3) link_BETA1-4 : bond 0.01182 ( 1) link_BETA1-4 : angle 4.63501 ( 3) hydrogen bonds : bond 0.04938 ( 142) hydrogen bonds : angle 6.79219 ( 384) SS BOND : bond 0.00542 ( 7) SS BOND : angle 1.09425 ( 14) covalent geometry : bond 0.00581 ( 5338) covalent geometry : angle 0.69472 ( 7253) *********************** 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 133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.590 Fit side-chains REVERT: F 77 SER cc_start: 0.8560 (m) cc_final: 0.8094 (p) REVERT: F 81 GLU cc_start: 0.8587 (pm20) cc_final: 0.8240 (pm20) REVERT: G 99 ASP cc_start: 0.8775 (t70) cc_final: 0.8360 (t70) REVERT: K 73 ASP cc_start: 0.8556 (t0) cc_final: 0.8288 (t0) outliers start: 8 outliers final: 7 residues processed: 129 average time/residue: 0.2050 time to fit residues: 32.7102 Evaluate side-chains 124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 73 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN J 34 ASN K 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072279 restraints weight = 11920.246| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.83 r_work: 0.2933 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5347 Z= 0.130 Angle : 0.609 8.727 7273 Z= 0.303 Chirality : 0.045 0.302 786 Planarity : 0.004 0.034 937 Dihedral : 6.412 48.217 779 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.95 % Allowed : 15.25 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.32), residues: 661 helix: -3.27 (0.75), residues: 33 sheet: -0.25 (0.31), residues: 289 loop : -1.54 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 PHE 0.013 0.001 PHE B 392 TYR 0.010 0.001 TYR B 495 ARG 0.006 0.001 ARG G 16 Details of bonding type rmsd link_NAG-ASN : bond 0.01161 ( 1) link_NAG-ASN : angle 4.50690 ( 3) link_BETA1-4 : bond 0.01261 ( 1) link_BETA1-4 : angle 4.50720 ( 3) hydrogen bonds : bond 0.03988 ( 142) hydrogen bonds : angle 5.96916 ( 384) SS BOND : bond 0.00355 ( 7) SS BOND : angle 0.63678 ( 14) covalent geometry : bond 0.00298 ( 5338) covalent geometry : angle 0.59495 ( 7253) *********************** 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 142 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 516 GLU cc_start: 0.7908 (mp0) cc_final: 0.6831 (mp0) REVERT: F 77 SER cc_start: 0.8521 (m) cc_final: 0.8075 (p) REVERT: F 81 GLU cc_start: 0.8610 (pm20) cc_final: 0.8212 (pm20) REVERT: F 82 ASP cc_start: 0.8332 (m-30) cc_final: 0.8103 (m-30) REVERT: G 99 ASP cc_start: 0.8663 (t70) cc_final: 0.8390 (t70) REVERT: K 73 ASP cc_start: 0.8524 (t0) cc_final: 0.8101 (t0) outliers start: 11 outliers final: 5 residues processed: 135 average time/residue: 0.2078 time to fit residues: 34.6570 Evaluate side-chains 123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 83 PHE Chi-restraints excluded: chain K residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.0170 chunk 47 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 43 optimal weight: 5.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.072573 restraints weight = 12247.282| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.92 r_work: 0.2929 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5347 Z= 0.118 Angle : 0.599 7.641 7273 Z= 0.296 Chirality : 0.044 0.289 786 Planarity : 0.003 0.033 937 Dihedral : 5.624 41.491 779 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.13 % Allowed : 17.91 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.32), residues: 661 helix: -3.25 (0.75), residues: 33 sheet: -0.14 (0.31), residues: 287 loop : -1.36 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS K 35 PHE 0.024 0.001 PHE B 392 TYR 0.010 0.001 TYR G 95 ARG 0.004 0.000 ARG G 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00904 ( 1) link_NAG-ASN : angle 4.09926 ( 3) link_BETA1-4 : bond 0.01103 ( 1) link_BETA1-4 : angle 4.65123 ( 3) hydrogen bonds : bond 0.03647 ( 142) hydrogen bonds : angle 5.54230 ( 384) SS BOND : bond 0.00299 ( 7) SS BOND : angle 0.62729 ( 14) covalent geometry : bond 0.00272 ( 5338) covalent geometry : angle 0.58616 ( 7253) *********************** 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 136 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 516 GLU cc_start: 0.7983 (mp0) cc_final: 0.6895 (mp0) REVERT: F 77 SER cc_start: 0.8494 (m) cc_final: 0.8042 (p) REVERT: F 81 GLU cc_start: 0.8580 (pm20) cc_final: 0.8197 (pm20) REVERT: F 82 ASP cc_start: 0.8311 (m-30) cc_final: 0.8091 (m-30) REVERT: G 99 ASP cc_start: 0.8694 (t70) cc_final: 0.8323 (t70) REVERT: J 4 MET cc_start: 0.7954 (mmm) cc_final: 0.7752 (tpp) REVERT: K 73 ASP cc_start: 0.8522 (t0) cc_final: 0.8126 (t0) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.1868 time to fit residues: 30.6864 Evaluate side-chains 124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain F residue 22 THR 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 49 SER 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 16 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.0000 chunk 56 optimal weight: 0.8980 overall best weight: 0.9846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.070922 restraints weight = 12056.644| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.85 r_work: 0.2902 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5347 Z= 0.172 Angle : 0.633 7.259 7273 Z= 0.314 Chirality : 0.045 0.281 786 Planarity : 0.004 0.035 937 Dihedral : 5.437 36.803 779 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.37 % Allowed : 17.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.32), residues: 661 helix: -3.24 (0.75), residues: 33 sheet: -0.12 (0.31), residues: 301 loop : -1.35 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 47 HIS 0.002 0.001 HIS K 35 PHE 0.024 0.001 PHE B 392 TYR 0.012 0.001 TYR B 495 ARG 0.003 0.000 ARG K 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 1) link_NAG-ASN : angle 3.98988 ( 3) link_BETA1-4 : bond 0.00888 ( 1) link_BETA1-4 : angle 4.84204 ( 3) hydrogen bonds : bond 0.03760 ( 142) hydrogen bonds : angle 5.42747 ( 384) SS BOND : bond 0.00415 ( 7) SS BOND : angle 0.78778 ( 14) covalent geometry : bond 0.00402 ( 5338) covalent geometry : angle 0.62006 ( 7253) *********************** 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: 19 poor density : 118 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8831 (t0) cc_final: 0.8626 (t0) REVERT: B 516 GLU cc_start: 0.8091 (mp0) cc_final: 0.6939 (mp0) REVERT: F 77 SER cc_start: 0.8516 (m) cc_final: 0.8071 (p) REVERT: F 81 GLU cc_start: 0.8605 (pm20) cc_final: 0.8208 (pm20) REVERT: F 82 ASP cc_start: 0.8349 (m-30) cc_final: 0.8094 (m-30) REVERT: G 99 ASP cc_start: 0.8736 (t70) cc_final: 0.8392 (t70) REVERT: K 32 TYR cc_start: 0.9085 (m-80) cc_final: 0.8873 (m-80) REVERT: K 73 ASP cc_start: 0.8554 (t0) cc_final: 0.8112 (t0) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 0.2032 time to fit residues: 32.7049 Evaluate side-chains 126 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP 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 109 SER 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 49 SER 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 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071511 restraints weight = 12036.972| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.85 r_work: 0.2916 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2505 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= 0.144 Angle : 0.604 6.762 7273 Z= 0.299 Chirality : 0.045 0.269 786 Planarity : 0.004 0.034 937 Dihedral : 5.152 32.351 779 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.66 % Allowed : 18.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.32), residues: 661 helix: -3.22 (0.75), residues: 33 sheet: -0.17 (0.31), residues: 291 loop : -1.33 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS K 35 PHE 0.017 0.001 PHE B 392 TYR 0.010 0.001 TYR B 495 ARG 0.006 0.000 ARG G 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 1) link_NAG-ASN : angle 3.71684 ( 3) link_BETA1-4 : bond 0.00939 ( 1) link_BETA1-4 : angle 4.76157 ( 3) hydrogen bonds : bond 0.03513 ( 142) hydrogen bonds : angle 5.25817 ( 384) SS BOND : bond 0.00375 ( 7) SS BOND : angle 0.70281 ( 14) covalent geometry : bond 0.00338 ( 5338) covalent geometry : angle 0.59160 ( 7253) *********************** 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 133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8792 (t0) cc_final: 0.8573 (t0) REVERT: B 516 GLU cc_start: 0.8110 (mp0) cc_final: 0.6979 (mp0) REVERT: F 77 SER cc_start: 0.8446 (m) cc_final: 0.7999 (p) REVERT: F 81 GLU cc_start: 0.8587 (pm20) cc_final: 0.8178 (pm20) REVERT: F 82 ASP cc_start: 0.8350 (m-30) cc_final: 0.8092 (m-30) REVERT: G 99 ASP cc_start: 0.8715 (t70) cc_final: 0.8381 (t70) REVERT: K 32 TYR cc_start: 0.9043 (m-80) cc_final: 0.8804 (m-80) REVERT: K 46 GLU cc_start: 0.8353 (tt0) cc_final: 0.8125 (mt-10) REVERT: K 73 ASP cc_start: 0.8527 (t0) cc_final: 0.8076 (t0) outliers start: 15 outliers final: 12 residues processed: 128 average time/residue: 0.2004 time to fit residues: 31.8920 Evaluate side-chains 127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 22 THR 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 49 SER 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 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072753 restraints weight = 11930.996| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.91 r_work: 0.2938 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5347 Z= 0.106 Angle : 0.588 7.173 7273 Z= 0.289 Chirality : 0.044 0.257 786 Planarity : 0.003 0.033 937 Dihedral : 4.812 27.976 779 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.13 % Allowed : 19.86 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.32), residues: 661 helix: -3.17 (0.76), residues: 33 sheet: 0.14 (0.32), residues: 269 loop : -1.36 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS K 35 PHE 0.013 0.001 PHE B 392 TYR 0.008 0.001 TYR K 95 ARG 0.006 0.001 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 1) link_NAG-ASN : angle 3.43719 ( 3) link_BETA1-4 : bond 0.00906 ( 1) link_BETA1-4 : angle 4.55288 ( 3) hydrogen bonds : bond 0.03227 ( 142) hydrogen bonds : angle 5.04546 ( 384) SS BOND : bond 0.00305 ( 7) SS BOND : angle 0.59684 ( 14) covalent geometry : bond 0.00245 ( 5338) covalent geometry : angle 0.57708 ( 7253) *********************** 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 131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8785 (t0) cc_final: 0.8453 (t0) REVERT: B 516 GLU cc_start: 0.8167 (mp0) cc_final: 0.7043 (mp0) REVERT: F 77 SER cc_start: 0.8428 (m) cc_final: 0.7982 (p) REVERT: F 81 GLU cc_start: 0.8562 (pm20) cc_final: 0.8162 (pm20) REVERT: F 82 ASP cc_start: 0.8315 (m-30) cc_final: 0.8061 (m-30) REVERT: G 99 ASP cc_start: 0.8711 (t70) cc_final: 0.8398 (t70) REVERT: K 73 ASP cc_start: 0.8480 (t0) cc_final: 0.8045 (t0) outliers start: 12 outliers final: 10 residues processed: 127 average time/residue: 0.2035 time to fit residues: 32.3475 Evaluate side-chains 126 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 518 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 22 THR 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 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071651 restraints weight = 12108.175| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.91 r_work: 0.2915 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2650 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= 0.148 Angle : 0.607 6.913 7273 Z= 0.301 Chirality : 0.044 0.256 786 Planarity : 0.004 0.033 937 Dihedral : 4.819 25.235 779 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.01 % Allowed : 19.33 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.32), residues: 661 helix: -3.22 (0.74), residues: 33 sheet: 0.12 (0.31), residues: 283 loop : -1.37 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 47 HIS 0.002 0.001 HIS K 35 PHE 0.014 0.001 PHE B 392 TYR 0.010 0.001 TYR K 32 ARG 0.006 0.001 ARG K 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 1) link_NAG-ASN : angle 3.44771 ( 3) link_BETA1-4 : bond 0.00787 ( 1) link_BETA1-4 : angle 4.50283 ( 3) hydrogen bonds : bond 0.03349 ( 142) hydrogen bonds : angle 5.10106 ( 384) SS BOND : bond 0.00392 ( 7) SS BOND : angle 0.74647 ( 14) covalent geometry : bond 0.00350 ( 5338) covalent geometry : angle 0.59608 ( 7253) *********************** 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 136 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8830 (t0) cc_final: 0.8501 (t0) REVERT: B 516 GLU cc_start: 0.8194 (mp0) cc_final: 0.7114 (mp0) REVERT: F 77 SER cc_start: 0.8431 (m) cc_final: 0.7984 (p) REVERT: F 81 GLU cc_start: 0.8568 (pm20) cc_final: 0.8160 (pm20) REVERT: F 82 ASP cc_start: 0.8357 (m-30) cc_final: 0.8085 (m-30) REVERT: G 99 ASP cc_start: 0.8734 (t70) cc_final: 0.8417 (t70) REVERT: K 73 ASP cc_start: 0.8533 (t0) cc_final: 0.8084 (t0) outliers start: 17 outliers final: 15 residues processed: 130 average time/residue: 0.1972 time to fit residues: 32.2142 Evaluate side-chains 133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 430 THR 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 17 ASP Chi-restraints excluded: chain F residue 22 THR 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 16 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.072725 restraints weight = 12130.006| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.93 r_work: 0.2935 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2715 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= 0.120 Angle : 0.601 7.026 7273 Z= 0.298 Chirality : 0.044 0.246 786 Planarity : 0.003 0.033 937 Dihedral : 4.646 21.726 779 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.19 % Allowed : 20.04 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.32), residues: 661 helix: -3.23 (0.74), residues: 33 sheet: 0.19 (0.32), residues: 269 loop : -1.32 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS K 35 PHE 0.011 0.001 PHE B 392 TYR 0.009 0.001 TYR K 32 ARG 0.006 0.000 ARG K 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 1) link_NAG-ASN : angle 3.23042 ( 3) link_BETA1-4 : bond 0.00742 ( 1) link_BETA1-4 : angle 4.28108 ( 3) hydrogen bonds : bond 0.03171 ( 142) hydrogen bonds : angle 5.01099 ( 384) SS BOND : bond 0.00313 ( 7) SS BOND : angle 0.73516 ( 14) covalent geometry : bond 0.00283 ( 5338) covalent geometry : angle 0.59114 ( 7253) *********************** 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 138 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8802 (t0) cc_final: 0.8487 (t0) REVERT: B 516 GLU cc_start: 0.8199 (mp0) cc_final: 0.7128 (mp0) REVERT: F 77 SER cc_start: 0.8413 (m) cc_final: 0.7969 (p) REVERT: F 81 GLU cc_start: 0.8556 (pm20) cc_final: 0.8155 (pm20) REVERT: F 82 ASP cc_start: 0.8315 (m-30) cc_final: 0.8050 (m-30) REVERT: G 99 ASP cc_start: 0.8737 (t70) cc_final: 0.8420 (t70) REVERT: K 73 ASP cc_start: 0.8508 (t0) cc_final: 0.8042 (t0) outliers start: 18 outliers final: 15 residues processed: 132 average time/residue: 0.1944 time to fit residues: 32.1324 Evaluate side-chains 134 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 430 THR 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 17 ASP Chi-restraints excluded: chain F residue 22 THR 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 24 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.070469 restraints weight = 12180.724| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.90 r_work: 0.2885 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5347 Z= 0.200 Angle : 0.657 7.040 7273 Z= 0.330 Chirality : 0.046 0.248 786 Planarity : 0.004 0.035 937 Dihedral : 4.972 21.713 779 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.84 % Allowed : 20.04 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.32), residues: 661 helix: -3.35 (0.70), residues: 33 sheet: -0.10 (0.30), residues: 304 loop : -1.22 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 47 HIS 0.003 0.001 HIS K 35 PHE 0.013 0.001 PHE B 392 TYR 0.021 0.002 TYR F 49 ARG 0.006 0.001 ARG K 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 1) link_NAG-ASN : angle 3.30026 ( 3) link_BETA1-4 : bond 0.00650 ( 1) link_BETA1-4 : angle 4.22977 ( 3) hydrogen bonds : bond 0.03595 ( 142) hydrogen bonds : angle 5.24188 ( 384) SS BOND : bond 0.00458 ( 7) SS BOND : angle 0.99287 ( 14) covalent geometry : bond 0.00471 ( 5338) covalent geometry : angle 0.64751 ( 7253) ********************** 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 130 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: B 360 ASN cc_start: 0.8864 (t0) cc_final: 0.8531 (t0) REVERT: B 370 ASN cc_start: 0.8675 (p0) cc_final: 0.8462 (p0) REVERT: F 77 SER cc_start: 0.8439 (m) cc_final: 0.7988 (p) REVERT: F 81 GLU cc_start: 0.8593 (pm20) cc_final: 0.8183 (pm20) REVERT: F 82 ASP cc_start: 0.8419 (m-30) cc_final: 0.8137 (m-30) REVERT: G 99 ASP cc_start: 0.8755 (t70) cc_final: 0.8404 (t70) REVERT: J 3 GLN cc_start: 0.8078 (mp10) cc_final: 0.7799 (mp10) REVERT: J 104 LYS cc_start: 0.8749 (tmtt) cc_final: 0.8494 (tmtt) REVERT: K 73 ASP cc_start: 0.8572 (t0) cc_final: 0.8095 (t0) outliers start: 16 outliers final: 13 residues processed: 127 average time/residue: 0.2073 time to fit residues: 32.6122 Evaluate side-chains 127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 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 21 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.071769 restraints weight = 12187.016| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.93 r_work: 0.2920 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5347 Z= 0.131 Angle : 0.618 6.882 7273 Z= 0.308 Chirality : 0.045 0.236 786 Planarity : 0.004 0.034 937 Dihedral : 4.752 21.436 779 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.84 % Allowed : 20.21 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.32), residues: 661 helix: -3.33 (0.70), residues: 33 sheet: 0.10 (0.31), residues: 274 loop : -1.34 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS K 35 PHE 0.010 0.001 PHE B 392 TYR 0.009 0.001 TYR K 32 ARG 0.007 0.001 ARG G 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 1) link_NAG-ASN : angle 2.99858 ( 3) link_BETA1-4 : bond 0.00694 ( 1) link_BETA1-4 : angle 3.93152 ( 3) hydrogen bonds : bond 0.03236 ( 142) hydrogen bonds : angle 5.10776 ( 384) SS BOND : bond 0.00348 ( 7) SS BOND : angle 0.77626 ( 14) covalent geometry : bond 0.00307 ( 5338) covalent geometry : angle 0.60950 ( 7253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.32 seconds wall clock time: 59 minutes 35.09 seconds (3575.09 seconds total)