Starting phenix.real_space_refine on Mon Jan 20 07:36:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xky_38431/01_2025/8xky_38431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xky_38431/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xky_38431/01_2025/8xky_38431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xky_38431/01_2025/8xky_38431.map" model { file = "/net/cci-nas-00/data/ceres_data/8xky_38431/01_2025/8xky_38431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xky_38431/01_2025/8xky_38431.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: I, F, J, G, H Time building chain proxies: 11.13, per 1000 atoms: 0.75 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: 3.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.09 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: 8.23 Time building geometry restraints manager: 4.39 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: 0.04 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } 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: 0.780 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: 0.240 Extract box with map and model: 0.540 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 39.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- 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= 0.361 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (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 TRP 0.006 0.001 TRP E 32 HIS 0.004 0.001 HIS C 43 PHE 0.029 0.001 PHE G 130 TYR 0.004 0.001 TYR J 30 ARG 0.001 0.000 ARG A 310 *********************** 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 : 1.220 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: 0.4230 time to fit residues: 63.6842 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 : 1.213 ------------------------------------------------------------------------------- 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 77 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.076592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.066869 restraints weight = 177253.799| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.44 r_work: 0.3242 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 7760 Z= 0.377 Angle : 0.809 13.740 10520 Z= 0.429 Chirality : 0.061 0.457 1188 Planarity : 0.005 0.039 1344 Dihedral : 4.326 27.215 1020 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.94 % Allowed : 19.28 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 944 helix: 2.56 (0.28), residues: 348 sheet: 0.11 (0.27), residues: 390 loop : -1.32 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.002 0.001 HIS F 346 PHE 0.015 0.001 PHE F 187 TYR 0.007 0.001 TYR F 217 ARG 0.003 0.000 ARG A 140 *********************** 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 135 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 1.185 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 outliers start: 41 outliers final: 30 residues processed: 108 average time/residue: 0.4624 time to fit residues: 67.5827 Evaluate side-chains 120 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 128 LYS 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 55 ASP 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 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 127 GLU Chi-restraints excluded: chain G residue 128 LYS 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 75 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.065184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055613 restraints weight = 139279.329| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.56 r_work: 0.3231 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7760 Z= 0.177 Angle : 0.735 27.089 10520 Z= 0.357 Chirality : 0.060 0.455 1188 Planarity : 0.004 0.037 1344 Dihedral : 3.881 14.617 1016 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.93 % Allowed : 20.48 % Favored : 77.59 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.29), residues: 944 helix: 2.81 (0.27), residues: 348 sheet: -0.28 (0.26), residues: 404 loop : -0.69 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.003 0.001 HIS C 43 PHE 0.008 0.001 PHE F 126 TYR 0.006 0.001 TYR F 171 ARG 0.004 0.000 ARG A 140 *********************** 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 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.273 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: D 56 MET cc_start: 0.9120 (tpp) cc_final: 0.8419 (tpp) outliers start: 16 outliers final: 16 residues processed: 98 average time/residue: 0.4199 time to fit residues: 56.8483 Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 0.0470 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.064484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054921 restraints weight = 140238.205| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.54 r_work: 0.3262 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2200 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= 0.208 Angle : 0.710 26.615 10520 Z= 0.343 Chirality : 0.059 0.460 1188 Planarity : 0.003 0.034 1344 Dihedral : 3.806 15.690 1016 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.93 % Allowed : 21.08 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.29), residues: 944 helix: 2.87 (0.27), residues: 348 sheet: -0.14 (0.27), residues: 390 loop : -1.01 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 36 HIS 0.004 0.001 HIS F 102 PHE 0.005 0.001 PHE F 126 TYR 0.005 0.001 TYR F 171 ARG 0.003 0.000 ARG A 140 *********************** 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 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.129 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: D 56 MET cc_start: 0.9120 (tpp) cc_final: 0.8418 (tpp) REVERT: A 64 GLU cc_start: 0.9418 (tp30) cc_final: 0.9009 (tm-30) REVERT: F 64 GLU cc_start: 0.9433 (tp30) cc_final: 0.9024 (tm-30) outliers start: 16 outliers final: 16 residues processed: 100 average time/residue: 0.3939 time to fit residues: 54.8310 Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 A residue 233 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.076813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067193 restraints weight = 176684.007| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.48 r_work: 0.3212 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7760 Z= 0.154 Angle : 0.706 26.720 10520 Z= 0.338 Chirality : 0.059 0.460 1188 Planarity : 0.003 0.034 1344 Dihedral : 3.717 16.494 1016 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 21.69 % Favored : 76.39 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.29), residues: 944 helix: 2.94 (0.27), residues: 348 sheet: -0.37 (0.26), residues: 404 loop : -0.54 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 41 HIS 0.002 0.001 HIS C 43 PHE 0.004 0.001 PHE F 359 TYR 0.006 0.001 TYR A 232 ARG 0.002 0.000 ARG A 140 *********************** 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 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.371 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: B 122 GLN cc_start: 0.9588 (mt0) cc_final: 0.9253 (tm-30) REVERT: D 56 MET cc_start: 0.9083 (tpp) cc_final: 0.8361 (tpp) REVERT: A 64 GLU cc_start: 0.9363 (tp30) cc_final: 0.8973 (tm-30) REVERT: G 122 GLN cc_start: 0.9608 (mt0) cc_final: 0.9232 (tm-30) REVERT: F 64 GLU cc_start: 0.9362 (tp30) cc_final: 0.8968 (tm-30) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.3911 time to fit residues: 55.2803 Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 VAL 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 E residue 51 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 VAL 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 J residue 51 LEU Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.064001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.054449 restraints weight = 142719.637| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.55 r_work: 0.3210 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7760 Z= 0.189 Angle : 0.689 26.576 10520 Z= 0.330 Chirality : 0.059 0.462 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.669 17.230 1016 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.69 % Allowed : 21.81 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 944 helix: 3.07 (0.27), residues: 348 sheet: -0.11 (0.26), residues: 390 loop : -0.87 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 PHE 0.004 0.001 PHE A 120 TYR 0.004 0.001 TYR A 171 ARG 0.001 0.000 ARG F 310 *********************** 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 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.236 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: D 56 MET cc_start: 0.9129 (tpp) cc_final: 0.8389 (tpp) REVERT: A 64 GLU cc_start: 0.9400 (tp30) cc_final: 0.9019 (tm-30) REVERT: I 56 MET cc_start: 0.8910 (tpp) cc_final: 0.8202 (tpp) REVERT: F 64 GLU cc_start: 0.9393 (tp30) cc_final: 0.9000 (tm-30) outliers start: 14 outliers final: 14 residues processed: 95 average time/residue: 0.3499 time to fit residues: 48.4215 Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 VAL 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 E residue 51 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.060904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.051783 restraints weight = 142079.499| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.62 r_work: 0.3153 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7760 Z= 0.213 Angle : 0.705 26.487 10520 Z= 0.338 Chirality : 0.059 0.463 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.669 17.359 1016 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.53 % Allowed : 21.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 944 helix: 3.09 (0.27), residues: 348 sheet: -0.07 (0.27), residues: 388 loop : -0.88 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 41 HIS 0.003 0.001 HIS F 102 PHE 0.004 0.001 PHE F 126 TYR 0.004 0.001 TYR A 171 ARG 0.001 0.000 ARG F 219 *********************** 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 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.282 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: B 126 MET cc_start: 0.9340 (tpp) cc_final: 0.9088 (tpp) REVERT: D 56 MET cc_start: 0.9094 (tpp) cc_final: 0.8351 (tpp) REVERT: A 64 GLU cc_start: 0.9443 (tp30) cc_final: 0.9075 (tm-30) REVERT: I 56 MET cc_start: 0.8933 (tpp) cc_final: 0.8347 (tpp) REVERT: F 64 GLU cc_start: 0.9418 (tp30) cc_final: 0.9045 (tm-30) outliers start: 21 outliers final: 19 residues processed: 96 average time/residue: 0.3382 time to fit residues: 46.6238 Evaluate side-chains 106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 37 LEU 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 214 GLU Chi-restraints excluded: chain A residue 233 LEU 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 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 214 GLU Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.065131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055156 restraints weight = 148212.973| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 4.55 r_work: 0.3209 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7760 Z= 0.195 Angle : 0.718 26.378 10520 Z= 0.340 Chirality : 0.060 0.464 1188 Planarity : 0.003 0.034 1344 Dihedral : 3.664 18.424 1016 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.29 % Allowed : 22.53 % Favored : 75.18 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 944 helix: 3.09 (0.27), residues: 348 sheet: -0.08 (0.26), residues: 388 loop : -0.90 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 PHE 0.005 0.001 PHE A 98 TYR 0.005 0.001 TYR F 171 ARG 0.002 0.000 ARG F 310 *********************** 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 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.222 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: A 64 GLU cc_start: 0.9470 (tp30) cc_final: 0.9076 (tm-30) REVERT: G 126 MET cc_start: 0.9421 (tpp) cc_final: 0.9147 (tpp) REVERT: I 56 MET cc_start: 0.8979 (tpp) cc_final: 0.8397 (tpp) REVERT: F 64 GLU cc_start: 0.9459 (tp30) cc_final: 0.9061 (tm-30) outliers start: 19 outliers final: 18 residues processed: 94 average time/residue: 0.3464 time to fit residues: 47.1157 Evaluate side-chains 106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 37 LEU 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 214 GLU Chi-restraints excluded: chain A residue 233 LEU 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 I residue 37 LEU 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 214 GLU 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 68 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.061815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.053056 restraints weight = 142770.053| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.67 r_work: 0.3232 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3070 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= 0.201 Angle : 0.718 26.379 10520 Z= 0.341 Chirality : 0.060 0.471 1188 Planarity : 0.003 0.035 1344 Dihedral : 3.660 18.116 1016 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.41 % Allowed : 22.29 % Favored : 75.30 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.29), residues: 944 helix: 3.09 (0.27), residues: 348 sheet: -0.06 (0.27), residues: 388 loop : -0.94 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 PHE 0.005 0.001 PHE A 98 TYR 0.004 0.001 TYR A 171 ARG 0.008 0.000 ARG F 52 *********************** 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 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.158 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: A 64 GLU cc_start: 0.9510 (tp30) cc_final: 0.9095 (tm-30) REVERT: I 56 MET cc_start: 0.8969 (tpp) cc_final: 0.8401 (tpp) REVERT: F 64 GLU cc_start: 0.9486 (tp30) cc_final: 0.9084 (tm-30) outliers start: 20 outliers final: 20 residues processed: 96 average time/residue: 0.3729 time to fit residues: 51.8826 Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 19 GLU 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 E residue 51 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 233 LEU 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 I residue 37 LEU 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 214 GLU 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 20 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 32 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.064874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054933 restraints weight = 148049.666| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.57 r_work: 0.3221 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7760 Z= 0.175 Angle : 0.721 26.426 10520 Z= 0.339 Chirality : 0.060 0.479 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.626 18.985 1016 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.17 % Allowed : 22.65 % Favored : 75.18 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 944 helix: 3.13 (0.27), residues: 348 sheet: -0.04 (0.27), residues: 388 loop : -0.89 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP J 41 HIS 0.002 0.001 HIS F 102 PHE 0.006 0.001 PHE A 98 TYR 0.004 0.000 TYR A 171 ARG 0.002 0.000 ARG F 310 ********************** 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 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.225 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: B 126 MET cc_start: 0.9436 (tpp) cc_final: 0.9193 (tpp) REVERT: A 64 GLU cc_start: 0.9454 (tp30) cc_final: 0.9041 (tm-30) REVERT: I 56 MET cc_start: 0.9003 (tpp) cc_final: 0.8426 (tpp) REVERT: F 64 GLU cc_start: 0.9466 (tp30) cc_final: 0.9057 (tm-30) outliers start: 18 outliers final: 18 residues processed: 99 average time/residue: 0.3426 time to fit residues: 48.7532 Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 19 GLU 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 E residue 51 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain A residue 233 LEU 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 I residue 37 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.075805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.066015 restraints weight = 176295.918| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.45 r_work: 0.3214 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3267 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= 0.210 Angle : 0.716 26.270 10520 Z= 0.340 Chirality : 0.059 0.466 1188 Planarity : 0.003 0.034 1344 Dihedral : 3.630 18.547 1016 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.41 % Allowed : 22.17 % Favored : 75.42 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 944 helix: 3.08 (0.27), residues: 348 sheet: -0.03 (0.27), residues: 388 loop : -0.88 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 PHE 0.005 0.001 PHE A 98 TYR 0.003 0.001 TYR A 171 ARG 0.002 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.99 seconds wall clock time: 115 minutes 12.16 seconds (6912.16 seconds total)