Starting phenix.real_space_refine on Fri Aug 22 15:33:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0h_28757/08_2025/8f0h_28757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0h_28757/08_2025/8f0h_28757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f0h_28757/08_2025/8f0h_28757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0h_28757/08_2025/8f0h_28757.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0h_28757/08_2025/8f0h_28757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0h_28757/08_2025/8f0h_28757.cif" } resolution = 3.18 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= -0.000 sd= 0.010 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 24 5.16 5 C 3134 2.51 5 N 839 2.21 5 O 962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4959 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 960 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Conformer: "A" Number of residues, atoms: 123, 958 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 976 Chain: "C" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1528 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 887 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.58, per 1000 atoms: 0.32 Number of scatterers: 4959 At special positions: 0 Unit cell: (67.1, 110, 92.4, 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 24 16.00 O 962 8.00 N 839 7.00 C 3134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 M 1 " - " NAG M 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG M 1 " - " ASN C 343 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 206.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 14 sheets defined 8.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.729A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.453A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.612A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.232A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.678A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.543A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.709A pdb=" N GLY B 50 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 60 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 48 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 94 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.669A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.382A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 47 removed outlier: 5.303A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP D 91 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS D 96 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.956A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.158A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.599A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 405 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: 0.68 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1594 1.34 - 1.46: 1215 1.46 - 1.58: 2244 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5084 Sorted by residual: bond pdb=" N ILE L 75 " pdb=" CA ILE L 75 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" N THR L 72 " pdb=" CA THR L 72 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.53e+00 bond pdb=" N PHE L 73 " pdb=" CA PHE L 73 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.86e+00 bond pdb=" N THR L 74 " pdb=" CA THR L 74 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.77e+00 bond pdb=" N SER L 77 " pdb=" CA SER L 77 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.28e-02 6.10e+03 5.16e+00 ... (remaining 5079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 6641 1.07 - 2.14: 196 2.14 - 3.21: 54 3.21 - 4.28: 12 4.28 - 5.35: 5 Bond angle restraints: 6908 Sorted by residual: angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 114.56 109.83 4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" C ASN L 76 " pdb=" CA ASN L 76 " pdb=" CB ASN L 76 " ideal model delta sigma weight residual 117.23 112.26 4.97 1.36e+00 5.41e-01 1.34e+01 angle pdb=" N ILE L 75 " pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 113.07 108.17 4.90 1.36e+00 5.41e-01 1.30e+01 angle pdb=" CA LEU L 78 " pdb=" C LEU L 78 " pdb=" O LEU L 78 " ideal model delta sigma weight residual 122.37 118.24 4.13 1.15e+00 7.56e-01 1.29e+01 angle pdb=" N VAL B 64 " pdb=" CA VAL B 64 " pdb=" C VAL B 64 " ideal model delta sigma weight residual 106.21 109.83 -3.62 1.07e+00 8.73e-01 1.15e+01 ... (remaining 6903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 2936 23.94 - 47.88: 66 47.88 - 71.83: 6 71.83 - 95.77: 6 95.77 - 119.71: 1 Dihedral angle restraints: 3015 sinusoidal: 1205 harmonic: 1810 Sorted by residual: dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N ASN L 30 " pdb=" CA ASN L 30 " ideal model delta harmonic sigma weight residual 180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C2 FUC M 3 " pdb=" C1 FUC M 3 " pdb=" O5 FUC M 3 " pdb=" C5 FUC M 3 " ideal model delta sinusoidal sigma weight residual 57.68 -62.03 119.71 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C1 FUC M 3 " pdb=" C5 FUC M 3 " pdb=" O5 FUC M 3 " pdb=" C4 FUC M 3 " ideal model delta sinusoidal sigma weight residual 59.12 -34.07 93.19 1 3.00e+01 1.11e-03 1.13e+01 ... (remaining 3012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 575 0.042 - 0.085: 109 0.085 - 0.127: 54 0.127 - 0.169: 2 0.169 - 0.212: 1 Chirality restraints: 741 Sorted by residual: chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 9.14e-01 chirality pdb=" CA LEU L 78 " pdb=" N LEU L 78 " pdb=" C LEU L 78 " pdb=" CB LEU L 78 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 738 not shown) Planarity restraints: 893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO L 96 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO C 521 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 100 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 101 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 101 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 101 " 0.017 5.00e-02 4.00e+02 ... (remaining 890 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1089 2.78 - 3.31: 4566 3.31 - 3.84: 8336 3.84 - 4.37: 10055 4.37 - 4.90: 17201 Nonbonded interactions: 41247 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.352 3.040 nonbonded pdb=" OG SER C 469 " pdb=" OE1 GLU C 471 " model vdw 2.372 3.040 nonbonded pdb=" O PHE B 29 " pdb=" NH2 ARG B 72 " model vdw 2.378 3.120 ... (remaining 41242 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 11.040 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.660 Find NCS groups from input model: 0.030 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.003 0.035 5095 Z= 0.152 Angle : 0.506 5.351 6933 Z= 0.301 Chirality : 0.040 0.212 741 Planarity : 0.004 0.044 892 Dihedral : 10.682 119.710 1851 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.38 % Allowed : 4.71 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.58 (0.33), residues: 624 helix: -1.83 (1.16), residues: 21 sheet: 0.74 (0.40), residues: 176 loop : -0.84 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.018 0.001 TYR L 91 PHE 0.006 0.001 PHE H 67 TRP 0.005 0.001 TRP H 107 HIS 0.001 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5084) covalent geometry : angle 0.49993 ( 6908) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.51812 ( 16) hydrogen bonds : bond 0.26384 ( 154) hydrogen bonds : angle 10.71201 ( 405) link_BETA1-4 : bond 0.00800 ( 1) link_BETA1-4 : angle 2.58517 ( 3) link_BETA1-6 : bond 0.00833 ( 1) link_BETA1-6 : angle 1.98196 ( 3) link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 2.09562 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8246 (tp40) cc_final: 0.7955 (mm-40) REVERT: C 385 THR cc_start: 0.8740 (t) cc_final: 0.8464 (p) REVERT: D 77 VAL cc_start: 0.6240 (t) cc_final: 0.5989 (p) REVERT: H 59 TYR cc_start: 0.8847 (m-80) cc_final: 0.8627 (m-80) REVERT: L 82 ASP cc_start: 0.7534 (m-30) cc_final: 0.6658 (m-30) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.1002 time to fit residues: 21.7126 Evaluate side-chains 123 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 0.0050 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN H 104 HIS L 30 ASN L 34 ASN L 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.101609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080268 restraints weight = 10140.619| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.05 r_work: 0.3049 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5095 Z= 0.168 Angle : 0.705 10.796 6933 Z= 0.370 Chirality : 0.046 0.168 741 Planarity : 0.005 0.046 892 Dihedral : 8.378 103.418 760 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.26 % Allowed : 12.81 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.80 (0.33), residues: 624 helix: -3.00 (0.76), residues: 27 sheet: 0.56 (0.39), residues: 174 loop : -0.86 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 16 TYR 0.020 0.002 TYR B 80 PHE 0.024 0.002 PHE C 429 TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5084) covalent geometry : angle 0.68620 ( 6908) SS BOND : bond 0.00761 ( 8) SS BOND : angle 3.03878 ( 16) hydrogen bonds : bond 0.04549 ( 154) hydrogen bonds : angle 7.25133 ( 405) link_BETA1-4 : bond 0.00701 ( 1) link_BETA1-4 : angle 2.04639 ( 3) link_BETA1-6 : bond 0.01247 ( 1) link_BETA1-6 : angle 2.50380 ( 3) link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 1.81408 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8485 (tp40) cc_final: 0.8246 (mm-40) REVERT: B 95 TYR cc_start: 0.8402 (m-80) cc_final: 0.8038 (m-80) REVERT: C 471 GLU cc_start: 0.8069 (mp0) cc_final: 0.7754 (mp0) REVERT: D 34 TRP cc_start: 0.8690 (m100) cc_final: 0.8182 (m100) REVERT: D 52 ASP cc_start: 0.7844 (t0) cc_final: 0.7429 (t0) REVERT: D 73 THR cc_start: 0.8275 (m) cc_final: 0.7921 (p) REVERT: D 91 ASP cc_start: 0.7589 (t0) cc_final: 0.7310 (t0) REVERT: H 26 GLU cc_start: 0.7301 (tp30) cc_final: 0.7058 (mt-10) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.0967 time to fit residues: 17.1908 Evaluate side-chains 127 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077938 restraints weight = 10184.050| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.09 r_work: 0.3017 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5095 Z= 0.170 Angle : 0.681 11.879 6933 Z= 0.353 Chirality : 0.045 0.181 741 Planarity : 0.005 0.047 892 Dihedral : 8.026 94.259 760 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.39 % Allowed : 15.63 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.00 (0.32), residues: 624 helix: -3.35 (0.66), residues: 27 sheet: 0.45 (0.38), residues: 182 loop : -1.03 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 16 TYR 0.021 0.002 TYR B 80 PHE 0.012 0.001 PHE C 377 TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5084) covalent geometry : angle 0.66185 ( 6908) SS BOND : bond 0.00545 ( 8) SS BOND : angle 2.95221 ( 16) hydrogen bonds : bond 0.04113 ( 154) hydrogen bonds : angle 6.46505 ( 405) link_BETA1-4 : bond 0.00927 ( 1) link_BETA1-4 : angle 2.10064 ( 3) link_BETA1-6 : bond 0.01123 ( 1) link_BETA1-6 : angle 3.01321 ( 3) link_NAG-ASN : bond 0.00170 ( 1) link_NAG-ASN : angle 1.48923 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8517 (tp40) cc_final: 0.8291 (mm-40) REVERT: B 90 ASP cc_start: 0.8634 (m-30) cc_final: 0.8276 (m-30) REVERT: B 95 TYR cc_start: 0.8364 (m-80) cc_final: 0.7976 (m-80) REVERT: D 6 GLN cc_start: 0.7387 (pt0) cc_final: 0.6592 (pp30) REVERT: D 34 TRP cc_start: 0.8678 (m100) cc_final: 0.8271 (m100) REVERT: D 73 THR cc_start: 0.8256 (m) cc_final: 0.7961 (p) REVERT: D 91 ASP cc_start: 0.7583 (t0) cc_final: 0.7194 (t0) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.1123 time to fit residues: 18.9342 Evaluate side-chains 126 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN H 3 GLN H 104 HIS L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076998 restraints weight = 10306.494| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.16 r_work: 0.2992 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5095 Z= 0.185 Angle : 0.696 12.449 6933 Z= 0.359 Chirality : 0.045 0.156 741 Planarity : 0.005 0.050 892 Dihedral : 7.688 85.717 760 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.52 % Allowed : 16.01 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.10 (0.32), residues: 624 helix: -3.05 (0.70), residues: 27 sheet: 0.39 (0.39), residues: 176 loop : -1.12 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 16 TYR 0.020 0.002 TYR B 80 PHE 0.011 0.001 PHE H 79 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 5084) covalent geometry : angle 0.67585 ( 6908) SS BOND : bond 0.00920 ( 8) SS BOND : angle 3.10803 ( 16) hydrogen bonds : bond 0.03766 ( 154) hydrogen bonds : angle 6.11373 ( 405) link_BETA1-4 : bond 0.00873 ( 1) link_BETA1-4 : angle 2.15024 ( 3) link_BETA1-6 : bond 0.01282 ( 1) link_BETA1-6 : angle 3.30076 ( 3) link_NAG-ASN : bond 0.00213 ( 1) link_NAG-ASN : angle 1.37159 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.8517 (tp40) cc_final: 0.8243 (mm-40) REVERT: B 30 ASP cc_start: 0.8857 (p0) cc_final: 0.8458 (p0) REVERT: B 31 ASP cc_start: 0.8885 (t0) cc_final: 0.8285 (m-30) REVERT: B 87 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6584 (mtm180) REVERT: B 90 ASP cc_start: 0.8524 (m-30) cc_final: 0.8078 (m-30) REVERT: B 95 TYR cc_start: 0.8359 (m-80) cc_final: 0.8061 (m-80) REVERT: B 118 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8293 (mtmm) REVERT: C 386 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9216 (mmtt) REVERT: C 471 GLU cc_start: 0.7952 (mp0) cc_final: 0.7737 (mp0) REVERT: D 52 ASP cc_start: 0.7891 (m-30) cc_final: 0.7545 (m-30) REVERT: D 73 THR cc_start: 0.8424 (m) cc_final: 0.8156 (p) REVERT: D 91 ASP cc_start: 0.7602 (t0) cc_final: 0.7131 (t0) REVERT: D 95 ASP cc_start: 0.8459 (m-30) cc_final: 0.8227 (t0) REVERT: L 78 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7552 (tt) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.1114 time to fit residues: 18.2651 Evaluate side-chains 133 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 6 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076499 restraints weight = 10321.385| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.12 r_work: 0.2983 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5095 Z= 0.170 Angle : 0.675 12.751 6933 Z= 0.345 Chirality : 0.045 0.178 741 Planarity : 0.005 0.051 892 Dihedral : 7.112 72.037 760 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.95 % Allowed : 16.76 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.15 (0.32), residues: 624 helix: -3.16 (0.66), residues: 27 sheet: 0.22 (0.39), residues: 184 loop : -1.10 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.020 0.002 TYR B 80 PHE 0.011 0.001 PHE H 79 TRP 0.012 0.001 TRP D 34 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5084) covalent geometry : angle 0.65675 ( 6908) SS BOND : bond 0.00700 ( 8) SS BOND : angle 2.72044 ( 16) hydrogen bonds : bond 0.03660 ( 154) hydrogen bonds : angle 5.95909 ( 405) link_BETA1-4 : bond 0.00912 ( 1) link_BETA1-4 : angle 2.16166 ( 3) link_BETA1-6 : bond 0.01450 ( 1) link_BETA1-6 : angle 3.68881 ( 3) link_NAG-ASN : bond 0.00170 ( 1) link_NAG-ASN : angle 1.42918 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7375 (mp10) cc_final: 0.7135 (mp10) REVERT: B 13 GLN cc_start: 0.8479 (tp40) cc_final: 0.8274 (mm-40) REVERT: B 30 ASP cc_start: 0.8848 (p0) cc_final: 0.8590 (p0) REVERT: B 31 ASP cc_start: 0.8890 (t0) cc_final: 0.8368 (m-30) REVERT: B 76 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8791 (ptpp) REVERT: B 87 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.6613 (mtm-85) REVERT: B 89 GLU cc_start: 0.8566 (mp0) cc_final: 0.8169 (pm20) REVERT: B 90 ASP cc_start: 0.8373 (m-30) cc_final: 0.7769 (m-30) REVERT: B 95 TYR cc_start: 0.8337 (m-80) cc_final: 0.8122 (m-80) REVERT: C 471 GLU cc_start: 0.7930 (mp0) cc_final: 0.7666 (mp0) REVERT: C 509 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8433 (mtt180) REVERT: D 34 TRP cc_start: 0.8622 (m100) cc_final: 0.8209 (m100) REVERT: D 52 ASP cc_start: 0.8012 (m-30) cc_final: 0.7609 (m-30) REVERT: D 73 THR cc_start: 0.8371 (m) cc_final: 0.8136 (p) REVERT: D 91 ASP cc_start: 0.7645 (t0) cc_final: 0.7129 (t0) REVERT: D 95 ASP cc_start: 0.8461 (m-30) cc_final: 0.8220 (t0) REVERT: H 13 GLN cc_start: 0.6421 (tp40) cc_final: 0.5896 (mp10) outliers start: 21 outliers final: 14 residues processed: 131 average time/residue: 0.1099 time to fit residues: 17.3001 Evaluate side-chains 128 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.074263 restraints weight = 10575.128| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.13 r_work: 0.2948 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5095 Z= 0.251 Angle : 0.727 12.574 6933 Z= 0.373 Chirality : 0.046 0.172 741 Planarity : 0.006 0.053 892 Dihedral : 6.772 56.737 760 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.39 % Allowed : 17.33 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.29 (0.32), residues: 624 helix: -3.06 (0.69), residues: 27 sheet: 0.01 (0.38), residues: 184 loop : -1.15 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.024 0.002 TYR B 80 PHE 0.014 0.002 PHE H 67 TRP 0.012 0.002 TRP B 47 HIS 0.004 0.001 HIS H 104 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 5084) covalent geometry : angle 0.70896 ( 6908) SS BOND : bond 0.00782 ( 8) SS BOND : angle 2.69425 ( 16) hydrogen bonds : bond 0.03962 ( 154) hydrogen bonds : angle 6.03038 ( 405) link_BETA1-4 : bond 0.01016 ( 1) link_BETA1-4 : angle 2.45765 ( 3) link_BETA1-6 : bond 0.01462 ( 1) link_BETA1-6 : angle 4.21918 ( 3) link_NAG-ASN : bond 0.00147 ( 1) link_NAG-ASN : angle 1.45443 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7341 (mp10) cc_final: 0.7119 (mp10) REVERT: B 13 GLN cc_start: 0.8566 (tp40) cc_final: 0.8294 (mm-40) REVERT: B 30 ASP cc_start: 0.8909 (p0) cc_final: 0.8682 (p0) REVERT: B 31 ASP cc_start: 0.8917 (t0) cc_final: 0.8353 (m-30) REVERT: B 76 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8794 (ptpp) REVERT: B 87 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.6507 (mtm-85) REVERT: B 90 ASP cc_start: 0.8590 (m-30) cc_final: 0.7993 (m-30) REVERT: B 95 TYR cc_start: 0.8326 (m-80) cc_final: 0.8075 (m-80) REVERT: C 471 GLU cc_start: 0.7912 (mp0) cc_final: 0.7660 (mp0) REVERT: D 52 ASP cc_start: 0.8313 (m-30) cc_final: 0.7935 (m-30) REVERT: D 73 THR cc_start: 0.8468 (m) cc_final: 0.8193 (p) REVERT: D 91 ASP cc_start: 0.7804 (t0) cc_final: 0.7328 (t0) REVERT: L 55 GLU cc_start: 0.9019 (tp30) cc_final: 0.8750 (tp30) REVERT: L 78 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7787 (tt) outliers start: 18 outliers final: 14 residues processed: 126 average time/residue: 0.1047 time to fit residues: 16.0013 Evaluate side-chains 126 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 20 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.098931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076532 restraints weight = 10351.454| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.13 r_work: 0.2973 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5095 Z= 0.146 Angle : 0.675 11.814 6933 Z= 0.341 Chirality : 0.044 0.159 741 Planarity : 0.005 0.051 892 Dihedral : 6.232 55.957 760 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.20 % Allowed : 17.89 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.20 (0.32), residues: 624 helix: -3.07 (0.69), residues: 27 sheet: 0.08 (0.38), residues: 185 loop : -1.09 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.024 0.001 TYR B 80 PHE 0.010 0.001 PHE H 27 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5084) covalent geometry : angle 0.65681 ( 6908) SS BOND : bond 0.00637 ( 8) SS BOND : angle 2.41816 ( 16) hydrogen bonds : bond 0.03382 ( 154) hydrogen bonds : angle 5.90512 ( 405) link_BETA1-4 : bond 0.00954 ( 1) link_BETA1-4 : angle 2.45340 ( 3) link_BETA1-6 : bond 0.01634 ( 1) link_BETA1-6 : angle 4.63822 ( 3) link_NAG-ASN : bond 0.00200 ( 1) link_NAG-ASN : angle 1.29465 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7347 (mp10) cc_final: 0.7105 (mp10) REVERT: B 13 GLN cc_start: 0.8502 (tp40) cc_final: 0.8266 (mm-40) REVERT: B 30 ASP cc_start: 0.8931 (p0) cc_final: 0.8676 (p0) REVERT: B 31 ASP cc_start: 0.8903 (t0) cc_final: 0.8343 (m-30) REVERT: B 76 LYS cc_start: 0.9176 (ptpp) cc_final: 0.8855 (ptpp) REVERT: B 87 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.6464 (mtm-85) REVERT: B 90 ASP cc_start: 0.8384 (m-30) cc_final: 0.7723 (m-30) REVERT: C 471 GLU cc_start: 0.7862 (mp0) cc_final: 0.7610 (mp0) REVERT: D 52 ASP cc_start: 0.8172 (m-30) cc_final: 0.7790 (m-30) REVERT: D 91 ASP cc_start: 0.7714 (t0) cc_final: 0.7239 (t0) REVERT: D 95 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8670 (t0) REVERT: H 13 GLN cc_start: 0.6767 (tp40) cc_final: 0.6164 (mp10) REVERT: L 55 GLU cc_start: 0.8977 (tp30) cc_final: 0.8708 (tp30) outliers start: 17 outliers final: 15 residues processed: 123 average time/residue: 0.0964 time to fit residues: 14.4704 Evaluate side-chains 126 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 37 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075106 restraints weight = 10452.095| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.11 r_work: 0.2955 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5095 Z= 0.171 Angle : 0.675 11.460 6933 Z= 0.345 Chirality : 0.045 0.205 741 Planarity : 0.005 0.052 892 Dihedral : 5.550 55.442 760 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.01 % Allowed : 18.46 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.20 (0.32), residues: 624 helix: -3.04 (0.69), residues: 27 sheet: 0.12 (0.39), residues: 179 loop : -1.10 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 16 TYR 0.025 0.002 TYR B 80 PHE 0.010 0.001 PHE H 79 TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5084) covalent geometry : angle 0.65889 ( 6908) SS BOND : bond 0.00613 ( 8) SS BOND : angle 2.31337 ( 16) hydrogen bonds : bond 0.03452 ( 154) hydrogen bonds : angle 5.79711 ( 405) link_BETA1-4 : bond 0.00970 ( 1) link_BETA1-4 : angle 2.92049 ( 3) link_BETA1-6 : bond 0.00756 ( 1) link_BETA1-6 : angle 4.00050 ( 3) link_NAG-ASN : bond 0.00314 ( 1) link_NAG-ASN : angle 1.12250 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7377 (mp10) cc_final: 0.6966 (mp10) REVERT: B 13 GLN cc_start: 0.8573 (tp40) cc_final: 0.8297 (mm-40) REVERT: B 30 ASP cc_start: 0.8885 (p0) cc_final: 0.8601 (p0) REVERT: B 31 ASP cc_start: 0.8917 (t0) cc_final: 0.8331 (m-30) REVERT: B 76 LYS cc_start: 0.9171 (ptpp) cc_final: 0.8884 (ptpp) REVERT: B 87 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.6848 (mtm180) REVERT: B 90 ASP cc_start: 0.8439 (m-30) cc_final: 0.7781 (m-30) REVERT: B 102 ARG cc_start: 0.7752 (ptm160) cc_final: 0.7414 (ptm160) REVERT: C 471 GLU cc_start: 0.7821 (mp0) cc_final: 0.7452 (mp0) REVERT: D 52 ASP cc_start: 0.8296 (m-30) cc_final: 0.7849 (m-30) REVERT: D 73 THR cc_start: 0.8470 (m) cc_final: 0.8187 (p) REVERT: D 91 ASP cc_start: 0.7839 (t0) cc_final: 0.7397 (t0) REVERT: D 95 ASP cc_start: 0.8935 (t0) cc_final: 0.8672 (t0) REVERT: H 13 GLN cc_start: 0.6784 (tp40) cc_final: 0.6185 (mp10) REVERT: L 55 GLU cc_start: 0.8987 (tp30) cc_final: 0.8734 (tp30) REVERT: L 78 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7832 (tt) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.0974 time to fit residues: 15.4746 Evaluate side-chains 131 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.096749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074629 restraints weight = 10345.295| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.09 r_work: 0.2952 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5095 Z= 0.188 Angle : 0.688 11.477 6933 Z= 0.352 Chirality : 0.045 0.172 741 Planarity : 0.005 0.052 892 Dihedral : 5.472 54.771 760 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.39 % Allowed : 18.46 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.22 (0.32), residues: 624 helix: -3.01 (0.70), residues: 27 sheet: 0.08 (0.39), residues: 180 loop : -1.10 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.027 0.002 TYR B 80 PHE 0.011 0.001 PHE H 79 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5084) covalent geometry : angle 0.67576 ( 6908) SS BOND : bond 0.00641 ( 8) SS BOND : angle 2.32585 ( 16) hydrogen bonds : bond 0.03520 ( 154) hydrogen bonds : angle 5.82406 ( 405) link_BETA1-4 : bond 0.00843 ( 1) link_BETA1-4 : angle 2.89504 ( 3) link_BETA1-6 : bond 0.00059 ( 1) link_BETA1-6 : angle 1.49877 ( 3) link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 1.69526 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7221 (mp10) cc_final: 0.6886 (mp10) REVERT: B 30 ASP cc_start: 0.8874 (p0) cc_final: 0.8597 (p0) REVERT: B 31 ASP cc_start: 0.8941 (t0) cc_final: 0.8334 (m-30) REVERT: B 76 LYS cc_start: 0.9180 (ptpp) cc_final: 0.8889 (ptpp) REVERT: B 87 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.6875 (mtm180) REVERT: B 90 ASP cc_start: 0.8497 (m-30) cc_final: 0.7814 (m-30) REVERT: B 102 ARG cc_start: 0.7739 (ptm160) cc_final: 0.7481 (ptm160) REVERT: C 471 GLU cc_start: 0.7839 (mp0) cc_final: 0.7487 (mp0) REVERT: D 52 ASP cc_start: 0.8260 (m-30) cc_final: 0.7813 (m-30) REVERT: D 91 ASP cc_start: 0.7884 (t0) cc_final: 0.7440 (t0) REVERT: D 95 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8680 (t0) REVERT: H 11 LEU cc_start: 0.8370 (tp) cc_final: 0.7718 (pt) REVERT: H 13 GLN cc_start: 0.6763 (tp40) cc_final: 0.6177 (mp10) REVERT: L 55 GLU cc_start: 0.8980 (tp30) cc_final: 0.8722 (tp30) REVERT: L 78 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8016 (tt) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.0967 time to fit residues: 14.8890 Evaluate side-chains 133 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.0270 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN D 6 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075024 restraints weight = 10387.912| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.10 r_work: 0.2956 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5095 Z= 0.172 Angle : 0.671 11.246 6933 Z= 0.346 Chirality : 0.045 0.171 741 Planarity : 0.005 0.051 892 Dihedral : 5.496 55.665 760 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.01 % Allowed : 19.40 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.24 (0.32), residues: 624 helix: -2.99 (0.71), residues: 27 sheet: 0.06 (0.39), residues: 180 loop : -1.12 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 18 TYR 0.026 0.002 TYR B 80 PHE 0.010 0.001 PHE H 79 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5084) covalent geometry : angle 0.66011 ( 6908) SS BOND : bond 0.00628 ( 8) SS BOND : angle 2.25538 ( 16) hydrogen bonds : bond 0.03381 ( 154) hydrogen bonds : angle 5.77990 ( 405) link_BETA1-4 : bond 0.00783 ( 1) link_BETA1-4 : angle 2.55421 ( 3) link_BETA1-6 : bond 0.00169 ( 1) link_BETA1-6 : angle 1.38440 ( 3) link_NAG-ASN : bond 0.00244 ( 1) link_NAG-ASN : angle 1.57417 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 3 GLN cc_start: 0.7206 (mp10) cc_final: 0.6856 (mp10) REVERT: B 19 ARG cc_start: 0.8863 (ttt90) cc_final: 0.8523 (ttt90) REVERT: B 30 ASP cc_start: 0.8870 (p0) cc_final: 0.8594 (p0) REVERT: B 31 ASP cc_start: 0.8947 (t0) cc_final: 0.8321 (m-30) REVERT: B 76 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8915 (ptpp) REVERT: B 87 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7148 (mtm180) REVERT: B 90 ASP cc_start: 0.8506 (m-30) cc_final: 0.7804 (m-30) REVERT: C 471 GLU cc_start: 0.7805 (mp0) cc_final: 0.7463 (mp0) REVERT: D 52 ASP cc_start: 0.8253 (m-30) cc_final: 0.7838 (m-30) REVERT: D 91 ASP cc_start: 0.7881 (t0) cc_final: 0.7441 (t0) REVERT: D 95 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8634 (t0) REVERT: H 3 GLN cc_start: 0.7514 (tt0) cc_final: 0.7291 (tm-30) REVERT: H 11 LEU cc_start: 0.8356 (tp) cc_final: 0.7684 (pt) REVERT: H 13 GLN cc_start: 0.6766 (tp40) cc_final: 0.6178 (mp10) REVERT: L 55 GLU cc_start: 0.8969 (tp30) cc_final: 0.8713 (tp30) REVERT: L 78 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7996 (tt) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.0903 time to fit residues: 13.7696 Evaluate side-chains 132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.097893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075853 restraints weight = 10361.726| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.11 r_work: 0.2972 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5095 Z= 0.142 Angle : 0.647 10.780 6933 Z= 0.333 Chirality : 0.044 0.175 741 Planarity : 0.005 0.049 892 Dihedral : 5.407 55.014 760 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.01 % Allowed : 19.21 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.18 (0.32), residues: 624 helix: -2.95 (0.73), residues: 27 sheet: 0.09 (0.39), residues: 180 loop : -1.07 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 18 TYR 0.023 0.001 TYR B 80 PHE 0.012 0.001 PHE H 27 TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5084) covalent geometry : angle 0.63582 ( 6908) SS BOND : bond 0.00586 ( 8) SS BOND : angle 2.16223 ( 16) hydrogen bonds : bond 0.03217 ( 154) hydrogen bonds : angle 5.67910 ( 405) link_BETA1-4 : bond 0.00753 ( 1) link_BETA1-4 : angle 2.43808 ( 3) link_BETA1-6 : bond 0.00173 ( 1) link_BETA1-6 : angle 1.38276 ( 3) link_NAG-ASN : bond 0.00237 ( 1) link_NAG-ASN : angle 1.58163 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1687.00 seconds wall clock time: 29 minutes 38.05 seconds (1778.05 seconds total)