Starting phenix.real_space_refine on Thu Sep 18 07:15:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xky_38431/09_2025/8xky_38431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xky_38431/09_2025/8xky_38431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xky_38431/09_2025/8xky_38431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xky_38431/09_2025/8xky_38431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xky_38431/09_2025/8xky_38431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xky_38431/09_2025/8xky_38431.map" } resolution = 3.42 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= 0.006 sd= 0.044 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: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 4864 2.51 5 N 1272 2.21 5 O 1438 1.98 5 H 7332 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14928 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 782 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 638 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "D" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 540 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 854 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "A" Number of atoms: 4650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4650 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Restraints were copied for chains: G, H, I, J, F Time building chain proxies: 4.47, per 1000 atoms: 0.30 Number of scatterers: 14928 At special positions: 0 Unit cell: (126.14, 130.38, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 1438 8.00 N 1272 7.00 C 4864 6.00 H 7332 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 500.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 37.7% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 86 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 50 removed outlier: 3.593A pdb=" N THR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.897A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 44 removed outlier: 3.807A pdb=" N GLU E 15 " --> pdb=" O ASP E 11 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 30 " --> pdb=" O ASN E 26 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'A' and resid 50 through 56 removed outlier: 3.548A pdb=" N GLN A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 54 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 55 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 56 " --> pdb=" O GLN A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 56' Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'G' and resid 87 through 135 Proline residue: G 112 - end of helix Processing helix chain 'H' and resid 14 through 49 Proline residue: H 39 - end of helix Processing helix chain 'I' and resid 30 through 50 removed outlier: 3.593A pdb=" N THR I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE I 35 " --> pdb=" O PRO I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 58 removed outlier: 3.897A pdb=" N ASP I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 removed outlier: 3.807A pdb=" N GLU J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR J 30 " --> pdb=" O ASN J 26 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE J 33 " --> pdb=" O HIS J 29 " (cutoff:3.500A) Proline residue: J 34 - end of helix Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'F' and resid 50 through 56 removed outlier: 3.547A pdb=" N GLN F 53 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 54 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU F 56 " --> pdb=" O GLN F 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 50 through 56' Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.268A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 92 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 351 through 355 removed outlier: 4.268A pdb=" N LYS F 323 " --> pdb=" O ASP F 319 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR F 194 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS F 165 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE F 98 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE F 92 " --> pdb=" O PHE F 98 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE F 359 " --> pdb=" O ARG F 85 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP F 87 " --> pdb=" O PHE F 359 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR F 361 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN F 89 " --> pdb=" O THR F 361 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1488 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: 5.95 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 8.62: 15060 8.62 - 16.39: 26 16.39 - 24.17: 4 24.17 - 31.95: 0 31.95 - 39.72: 2 Warning: extremely large bond lengths. Bond restraints: 15092 Sorted by residual: bond pdb=" CB LYS A 352 " pdb=" HB1 LYS A 352 " ideal model delta sigma weight residual 0.970 39.724 -38.754 2.00e-02 2.50e+03 3.75e+06 bond pdb=" CB LYS F 352 " pdb=" HB1 LYS F 352 " ideal model delta sigma weight residual 0.970 39.724 -38.754 2.00e-02 2.50e+03 3.75e+06 bond pdb=" CB LEU I 61 " pdb=" HB1 LEU I 61 " ideal model delta sigma weight residual 0.970 18.686 -17.716 2.00e-02 2.50e+03 7.85e+05 bond pdb=" CB LEU D 61 " pdb=" HB1 LEU D 61 " ideal model delta sigma weight residual 0.970 18.685 -17.715 2.00e-02 2.50e+03 7.85e+05 bond pdb=" CB GLU B 127 " pdb=" HB1 GLU B 127 " ideal model delta sigma weight residual 0.970 18.429 -17.459 2.00e-02 2.50e+03 7.62e+05 ... (remaining 15087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.89: 26888 20.89 - 41.79: 146 41.79 - 62.68: 36 62.68 - 83.57: 18 83.57 - 104.47: 20 Bond angle restraints: 27108 Sorted by residual: angle pdb=" HB1 GLN G 121 " pdb=" CB GLN G 121 " pdb=" HB2 GLN G 121 " ideal model delta sigma weight residual 110.00 5.53 104.47 3.00e+00 1.11e-01 1.21e+03 angle pdb=" HB1 GLN B 121 " pdb=" CB GLN B 121 " pdb=" HB2 GLN B 121 " ideal model delta sigma weight residual 110.00 5.53 104.47 3.00e+00 1.11e-01 1.21e+03 angle pdb=" CB LYS B 128 " pdb=" CG LYS B 128 " pdb=" HG1 LYS B 128 " ideal model delta sigma weight residual 109.00 8.54 100.46 3.00e+00 1.11e-01 1.12e+03 angle pdb=" CB LYS G 128 " pdb=" CG LYS G 128 " pdb=" HG1 LYS G 128 " ideal model delta sigma weight residual 109.00 8.55 100.45 3.00e+00 1.11e-01 1.12e+03 angle pdb=" CD GLU A 64 " pdb=" CG GLU A 64 " pdb=" HG1 GLU A 64 " ideal model delta sigma weight residual 108.00 7.80 100.20 3.00e+00 1.11e-01 1.12e+03 ... (remaining 27103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6370 17.56 - 35.12: 618 35.12 - 52.67: 144 52.67 - 70.23: 34 70.23 - 87.79: 2 Dihedral angle restraints: 7168 sinusoidal: 3818 harmonic: 3350 Sorted by residual: dihedral pdb=" C LEU H 35 " pdb=" N LEU H 35 " pdb=" CA LEU H 35 " pdb=" CB LEU H 35 " ideal model delta harmonic sigma weight residual -122.60 -132.15 9.55 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C LEU C 35 " pdb=" N LEU C 35 " pdb=" CA LEU C 35 " pdb=" CB LEU C 35 " ideal model delta harmonic sigma weight residual -122.60 -132.15 9.55 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C ILE A 256 " pdb=" N ILE A 256 " pdb=" CA ILE A 256 " pdb=" CB ILE A 256 " ideal model delta harmonic sigma weight residual -122.00 -131.50 9.50 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 7165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1051 0.081 - 0.163: 115 0.163 - 0.244: 4 0.244 - 0.325: 2 0.325 - 0.407: 16 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CA HIS F 49 " pdb=" N HIS F 49 " pdb=" C HIS F 49 " pdb=" CB HIS F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA HIS A 49 " pdb=" N HIS A 49 " pdb=" C HIS A 49 " pdb=" CB HIS A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA ARG F 52 " pdb=" N ARG F 52 " pdb=" C ARG F 52 " pdb=" CB ARG F 52 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 1185 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 250 " 0.064 2.00e-02 2.50e+03 6.78e-02 6.89e+01 pdb=" CD GLN F 250 " -0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN F 250 " -0.062 2.00e-02 2.50e+03 pdb=" NE2 GLN F 250 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN F 250 " 0.100 2.00e-02 2.50e+03 pdb="HE22 GLN F 250 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 250 " -0.064 2.00e-02 2.50e+03 6.77e-02 6.88e+01 pdb=" CD GLN A 250 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN A 250 " 0.062 2.00e-02 2.50e+03 pdb=" NE2 GLN A 250 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 250 " -0.100 2.00e-02 2.50e+03 pdb="HE22 GLN A 250 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 122 " -0.064 2.00e-02 2.50e+03 6.67e-02 6.67e+01 pdb=" CG ASN F 122 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN F 122 " 0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN F 122 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN F 122 " -0.099 2.00e-02 2.50e+03 pdb="HD22 ASN F 122 " 0.096 2.00e-02 2.50e+03 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 216 2.04 - 2.68: 21773 2.68 - 3.32: 42209 3.32 - 3.96: 53119 3.96 - 4.60: 80500 Nonbonded interactions: 197817 Sorted by model distance: nonbonded pdb="HG21 VAL J 60 " pdb=" HB1 MET F 94 " model vdw 1.401 2.440 nonbonded pdb="HG21 VAL E 60 " pdb=" HB1 MET A 94 " model vdw 1.402 2.440 nonbonded pdb=" H ASP F 345 " pdb=" HA ASP F 345 " model vdw 1.577 1.816 nonbonded pdb=" H ASP A 345 " pdb=" HA ASP A 345 " model vdw 1.577 1.816 nonbonded pdb=" H SER F 50 " pdb=" HA SER F 50 " model vdw 1.579 1.816 ... (remaining 197812 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'F' } 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: 1.300 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: 0.060 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.006 0.126 7760 Z= 0.381 Angle : 0.848 10.516 10520 Z= 0.558 Chirality : 0.063 0.407 1188 Planarity : 0.005 0.046 1344 Dihedral : 15.241 87.791 2776 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.24 % Allowed : 20.96 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.37 (0.29), residues: 944 helix: 2.65 (0.27), residues: 348 sheet: 0.26 (0.27), residues: 400 loop : -0.78 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.004 0.001 TYR J 30 PHE 0.029 0.001 PHE G 130 TRP 0.006 0.001 TRP E 32 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 7760) covalent geometry : angle 0.84825 (10520) hydrogen bonds : bond 0.15905 ( 513) hydrogen bonds : angle 8.15543 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 110 average time/residue: 0.1930 time to fit residues: 28.9456 Evaluate side-chains 92 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain F residue 66 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.076310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.066518 restraints weight = 178751.250| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.48 r_work: 0.3142 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 7760 Z= 0.318 Angle : 0.827 14.315 10520 Z= 0.438 Chirality : 0.061 0.457 1188 Planarity : 0.005 0.039 1344 Dihedral : 4.339 28.163 1020 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.58 % Allowed : 20.12 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.29), residues: 944 helix: 2.57 (0.27), residues: 348 sheet: 0.07 (0.27), residues: 390 loop : -1.36 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.005 0.001 TYR F 217 PHE 0.014 0.001 PHE A 187 TRP 0.004 0.001 TRP C 36 HIS 0.002 0.001 HIS F 346 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 7760) covalent geometry : angle 0.82708 (10520) hydrogen bonds : bond 0.04905 ( 513) hydrogen bonds : angle 6.44675 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 106 average time/residue: 0.1982 time to fit residues: 27.9661 Evaluate side-chains 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 11 optimal weight: 50.0000 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN F 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.065818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.055714 restraints weight = 145335.940| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.69 r_work: 0.3196 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7760 Z= 0.156 Angle : 0.723 25.566 10520 Z= 0.357 Chirality : 0.059 0.456 1188 Planarity : 0.004 0.035 1344 Dihedral : 3.902 14.930 1016 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.41 % Allowed : 20.36 % Favored : 77.23 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.29), residues: 944 helix: 2.67 (0.28), residues: 348 sheet: -0.28 (0.26), residues: 404 loop : -0.85 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.006 0.001 TYR F 171 PHE 0.008 0.001 PHE F 126 TRP 0.004 0.001 TRP C 36 HIS 0.003 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7760) covalent geometry : angle 0.72281 (10520) hydrogen bonds : bond 0.03479 ( 513) hydrogen bonds : angle 5.77086 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 20 residues processed: 92 average time/residue: 0.1637 time to fit residues: 21.6513 Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 61 optimal weight: 0.0870 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.065650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055576 restraints weight = 144468.896| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 4.68 r_work: 0.3205 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7760 Z= 0.137 Angle : 0.715 26.702 10520 Z= 0.343 Chirality : 0.059 0.459 1188 Planarity : 0.003 0.034 1344 Dihedral : 3.777 16.487 1016 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.53 % Allowed : 20.84 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.29), residues: 944 helix: 2.66 (0.27), residues: 348 sheet: -0.33 (0.26), residues: 404 loop : -0.64 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 310 TYR 0.005 0.001 TYR F 171 PHE 0.005 0.001 PHE A 126 TRP 0.004 0.001 TRP H 36 HIS 0.003 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7760) covalent geometry : angle 0.71473 (10520) hydrogen bonds : bond 0.02979 ( 513) hydrogen bonds : angle 5.38553 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9409 (tp30) cc_final: 0.9048 (tm-30) REVERT: F 64 GLU cc_start: 0.9403 (tp30) cc_final: 0.9038 (tm-30) outliers start: 21 outliers final: 20 residues processed: 93 average time/residue: 0.1397 time to fit residues: 19.5319 Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.064609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055017 restraints weight = 141865.841| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.58 r_work: 0.3215 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7760 Z= 0.109 Angle : 0.720 27.046 10520 Z= 0.343 Chirality : 0.059 0.461 1188 Planarity : 0.003 0.034 1344 Dihedral : 3.680 17.062 1016 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.65 % Allowed : 21.20 % Favored : 76.14 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.29), residues: 944 helix: 2.78 (0.27), residues: 348 sheet: -0.26 (0.26), residues: 402 loop : -0.60 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 310 TYR 0.006 0.001 TYR A 79 PHE 0.005 0.001 PHE A 126 TRP 0.004 0.001 TRP J 41 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7760) covalent geometry : angle 0.71988 (10520) hydrogen bonds : bond 0.02771 ( 513) hydrogen bonds : angle 5.14733 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.8875 (tpp) cc_final: 0.8283 (tpp) REVERT: A 64 GLU cc_start: 0.9370 (tp30) cc_final: 0.8993 (tm-30) REVERT: I 56 MET cc_start: 0.8879 (tpp) cc_final: 0.8150 (tpp) REVERT: F 64 GLU cc_start: 0.9373 (tp30) cc_final: 0.9009 (tm-30) outliers start: 22 outliers final: 16 residues processed: 98 average time/residue: 0.1528 time to fit residues: 21.8157 Evaluate side-chains 101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 250 GLN Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 chunk 57 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 90 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.064990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055043 restraints weight = 145907.213| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.62 r_work: 0.3184 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7760 Z= 0.140 Angle : 0.704 27.205 10520 Z= 0.336 Chirality : 0.059 0.463 1188 Planarity : 0.003 0.031 1344 Dihedral : 3.633 18.125 1016 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.93 % Allowed : 21.81 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.29), residues: 944 helix: 2.94 (0.27), residues: 348 sheet: -0.01 (0.26), residues: 388 loop : -1.05 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.006 0.001 TYR A 232 PHE 0.003 0.001 PHE A 126 TRP 0.005 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7760) covalent geometry : angle 0.70413 (10520) hydrogen bonds : bond 0.02653 ( 513) hydrogen bonds : angle 4.94546 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.8914 (tpp) cc_final: 0.8319 (tpp) REVERT: A 64 GLU cc_start: 0.9398 (tp30) cc_final: 0.9032 (tm-30) REVERT: I 56 MET cc_start: 0.8927 (tpp) cc_final: 0.8338 (tpp) REVERT: F 64 GLU cc_start: 0.9389 (tp30) cc_final: 0.9021 (tm-30) outliers start: 16 outliers final: 14 residues processed: 92 average time/residue: 0.1411 time to fit residues: 19.4492 Evaluate side-chains 100 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN J 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.075768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.066260 restraints weight = 175797.851| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.43 r_work: 0.3234 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7760 Z= 0.136 Angle : 0.716 27.405 10520 Z= 0.339 Chirality : 0.060 0.464 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.644 18.084 1016 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.93 % Allowed : 21.81 % Favored : 76.27 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.29), residues: 944 helix: 2.93 (0.27), residues: 348 sheet: 0.01 (0.26), residues: 388 loop : -0.95 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 52 TYR 0.005 0.001 TYR F 79 PHE 0.005 0.001 PHE A 120 TRP 0.005 0.001 TRP E 41 HIS 0.002 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7760) covalent geometry : angle 0.71594 (10520) hydrogen bonds : bond 0.02644 ( 513) hydrogen bonds : angle 4.85691 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.8953 (tpp) cc_final: 0.8372 (tpp) REVERT: A 64 GLU cc_start: 0.9429 (tp30) cc_final: 0.9051 (tm-30) REVERT: G 126 MET cc_start: 0.9477 (mmm) cc_final: 0.9255 (mmm) REVERT: I 56 MET cc_start: 0.8916 (tpp) cc_final: 0.8340 (tpp) REVERT: F 64 GLU cc_start: 0.9436 (tp30) cc_final: 0.9039 (tm-30) outliers start: 16 outliers final: 16 residues processed: 91 average time/residue: 0.1431 time to fit residues: 19.3934 Evaluate side-chains 101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.060714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.051816 restraints weight = 144198.053| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.64 r_work: 0.3132 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7760 Z= 0.255 Angle : 0.753 27.323 10520 Z= 0.364 Chirality : 0.060 0.477 1188 Planarity : 0.004 0.040 1344 Dihedral : 3.812 18.857 1016 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.41 % Allowed : 21.57 % Favored : 76.02 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.29), residues: 944 helix: 2.80 (0.28), residues: 348 sheet: -0.02 (0.27), residues: 388 loop : -1.19 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 219 TYR 0.009 0.001 TYR A 307 PHE 0.007 0.001 PHE D 42 TRP 0.006 0.001 TRP F 145 HIS 0.005 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 7760) covalent geometry : angle 0.75344 (10520) hydrogen bonds : bond 0.02847 ( 513) hydrogen bonds : angle 4.95113 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.9069 (tpp) cc_final: 0.8512 (tpp) REVERT: I 56 MET cc_start: 0.9082 (tpp) cc_final: 0.8531 (tpp) outliers start: 20 outliers final: 16 residues processed: 90 average time/residue: 0.1417 time to fit residues: 19.2005 Evaluate side-chains 97 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.060380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.051519 restraints weight = 143307.844| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 4.51 r_work: 0.3228 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7760 Z= 0.199 Angle : 0.732 27.612 10520 Z= 0.350 Chirality : 0.060 0.461 1188 Planarity : 0.003 0.036 1344 Dihedral : 3.825 19.289 1016 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.69 % Allowed : 22.17 % Favored : 76.14 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.29), residues: 944 helix: 2.80 (0.28), residues: 348 sheet: -0.07 (0.27), residues: 388 loop : -1.09 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 219 TYR 0.006 0.001 TYR F 79 PHE 0.006 0.001 PHE A 98 TRP 0.005 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7760) covalent geometry : angle 0.73187 (10520) hydrogen bonds : bond 0.02695 ( 513) hydrogen bonds : angle 4.83393 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.9063 (tpp) cc_final: 0.8471 (tpp) REVERT: I 56 MET cc_start: 0.9064 (tpp) cc_final: 0.8476 (tpp) outliers start: 14 outliers final: 14 residues processed: 89 average time/residue: 0.1418 time to fit residues: 18.9426 Evaluate side-chains 96 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.060979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.052025 restraints weight = 141586.822| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.62 r_work: 0.3150 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7760 Z= 0.116 Angle : 0.730 27.733 10520 Z= 0.342 Chirality : 0.060 0.468 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.733 19.980 1016 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.57 % Allowed : 22.65 % Favored : 75.78 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.29), residues: 944 helix: 2.85 (0.28), residues: 348 sheet: -0.01 (0.27), residues: 388 loop : -0.87 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 310 TYR 0.005 0.001 TYR A 79 PHE 0.007 0.001 PHE A 98 TRP 0.005 0.001 TRP J 41 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7760) covalent geometry : angle 0.73031 (10520) hydrogen bonds : bond 0.02542 ( 513) hydrogen bonds : angle 4.69476 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.9029 (tpp) cc_final: 0.8451 (tpp) REVERT: I 56 MET cc_start: 0.9040 (tpp) cc_final: 0.8471 (tpp) REVERT: F 64 GLU cc_start: 0.9402 (tp30) cc_final: 0.9048 (tm-30) outliers start: 13 outliers final: 13 residues processed: 92 average time/residue: 0.1439 time to fit residues: 19.7146 Evaluate side-chains 98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.060788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.051931 restraints weight = 142700.010| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.53 r_work: 0.3241 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7760 Z= 0.176 Angle : 0.731 27.726 10520 Z= 0.347 Chirality : 0.060 0.465 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.733 19.182 1016 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.81 % Allowed : 22.65 % Favored : 75.54 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.29), residues: 944 helix: 2.85 (0.27), residues: 348 sheet: 0.01 (0.27), residues: 388 loop : -0.96 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 219 TYR 0.005 0.001 TYR A 79 PHE 0.006 0.001 PHE A 98 TRP 0.006 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7760) covalent geometry : angle 0.73135 (10520) hydrogen bonds : bond 0.02614 ( 513) hydrogen bonds : angle 4.71623 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.69 seconds wall clock time: 55 minutes 29.36 seconds (3329.36 seconds total)