Starting phenix.real_space_refine on Fri Jun 13 10:47:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xky_38431/06_2025/8xky_38431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xky_38431/06_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_38431/06_2025/8xky_38431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xky_38431/06_2025/8xky_38431.map" model { file = "/net/cci-nas-00/data/ceres_data/8xky_38431/06_2025/8xky_38431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xky_38431/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.43, per 1000 atoms: 0.77 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: 4.22 Conformation dependent library (CDL) restraints added in 1.4 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: 1.30 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: 9.62 Time building geometry restraints manager: 4.88 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: 0.05 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: 1.210 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: 0.260 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.570 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15905 ( 513) hydrogen bonds : angle 8.15543 ( 1488) covalent geometry : bond 0.00560 ( 7760) covalent geometry : angle 0.84825 (10520) *********************** 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 : 1.298 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: 0.4116 time to fit residues: 61.1410 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 : 1.201 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.066871 restraints weight = 177253.738| |-----------------------------------------------------------------------------| 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= 0.283 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 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 513) hydrogen bonds : angle 6.51282 ( 1488) covalent geometry : bond 0.00589 ( 7760) covalent geometry : angle 0.80865 (10520) *********************** 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 : 1.230 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: 0.4379 time to fit residues: 63.1511 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 : 1.524 ------------------------------------------------------------------------------- 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: 0.0980 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.065179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055599 restraints weight = 139336.467| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.55 r_work: 0.3227 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1930 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= 0.136 Angle : 0.727 25.971 10520 Z= 0.357 Chirality : 0.059 0.455 1188 Planarity : 0.004 0.037 1344 Dihedral : 3.890 14.418 1016 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.29 % Allowed : 20.36 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 944 helix: 2.79 (0.27), residues: 348 sheet: -0.28 (0.26), residues: 404 loop : -0.71 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.002 0.001 HIS C 43 PHE 0.007 0.001 PHE F 126 TYR 0.006 0.001 TYR F 171 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 513) hydrogen bonds : angle 5.81618 ( 1488) covalent geometry : bond 0.00279 ( 7760) covalent geometry : angle 0.72745 (10520) *********************** 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 115 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.571 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 outliers start: 19 outliers final: 19 residues processed: 98 average time/residue: 0.3985 time to fit residues: 53.8531 Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 55 ASP 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.064723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055156 restraints weight = 139551.766| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.55 r_work: 0.3235 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2176 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= 0.134 Angle : 0.713 26.989 10520 Z= 0.342 Chirality : 0.059 0.459 1188 Planarity : 0.003 0.036 1344 Dihedral : 3.793 15.727 1016 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.93 % Allowed : 21.45 % 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 (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: 1.14 (0.29), residues: 944 helix: 2.87 (0.27), residues: 348 sheet: -0.16 (0.27), residues: 390 loop : -1.00 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 36 HIS 0.003 0.001 HIS F 102 PHE 0.005 0.001 PHE A 126 TYR 0.005 0.001 TYR A 171 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 513) hydrogen bonds : angle 5.45194 ( 1488) covalent geometry : bond 0.00277 ( 7760) covalent geometry : angle 0.71253 (10520) *********************** 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 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.481 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 REVERT: D 56 MET cc_start: 0.9099 (tpp) cc_final: 0.8400 (tpp) REVERT: G 122 GLN cc_start: 0.9591 (mt0) cc_final: 0.9276 (tm-30) outliers start: 16 outliers final: 16 residues processed: 99 average time/residue: 0.3852 time to fit residues: 53.2452 Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.064113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.054581 restraints weight = 141699.860| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.52 r_work: 0.3215 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2497 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= 0.144 Angle : 0.699 26.409 10520 Z= 0.335 Chirality : 0.059 0.462 1188 Planarity : 0.003 0.034 1344 Dihedral : 3.716 16.398 1016 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.93 % Allowed : 21.93 % 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 (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: 1.21 (0.29), residues: 944 helix: 2.95 (0.27), residues: 348 sheet: -0.13 (0.26), residues: 390 loop : -0.99 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 41 HIS 0.003 0.001 HIS F 102 PHE 0.004 0.001 PHE F 120 TYR 0.005 0.001 TYR F 171 ARG 0.001 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 513) hydrogen bonds : angle 5.13778 ( 1488) covalent geometry : bond 0.00293 ( 7760) covalent geometry : angle 0.69896 (10520) *********************** 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 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.207 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: D 56 MET cc_start: 0.9109 (tpp) cc_final: 0.8382 (tpp) REVERT: A 64 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8891 (tm-30) REVERT: I 56 MET cc_start: 0.8922 (tpp) cc_final: 0.8192 (tpp) REVERT: F 64 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8879 (tm-30) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.3438 time to fit residues: 48.6062 Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 233 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: 3.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.064806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054605 restraints weight = 147861.158| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.71 r_work: 0.3182 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2724 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= 0.168 Angle : 0.700 26.586 10520 Z= 0.337 Chirality : 0.059 0.463 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.720 17.618 1016 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.93 % Allowed : 22.41 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 944 helix: 3.08 (0.27), residues: 348 sheet: -0.10 (0.26), residues: 388 loop : -1.01 (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 0.004 0.001 PHE F 120 TYR 0.004 0.001 TYR A 171 ARG 0.002 0.000 ARG F 310 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 513) hydrogen bonds : angle 4.96894 ( 1488) covalent geometry : bond 0.00341 ( 7760) covalent geometry : angle 0.69982 (10520) *********************** 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 109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.213 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: D 56 MET cc_start: 0.9156 (tpp) cc_final: 0.8417 (tpp) REVERT: A 64 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8896 (tm-30) REVERT: I 56 MET cc_start: 0.8936 (tpp) cc_final: 0.8348 (tpp) REVERT: F 64 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8895 (tm-30) outliers start: 16 outliers final: 14 residues processed: 99 average time/residue: 0.3307 time to fit residues: 47.4164 Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain G residue 102 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 0.0570 chunk 78 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.5502 ------------------------------------------------------------------------------- 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 ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.060967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.052183 restraints weight = 139526.290| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.52 r_work: 0.3169 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7760 Z= 0.098 Angle : 0.707 26.474 10520 Z= 0.333 Chirality : 0.060 0.467 1188 Planarity : 0.003 0.033 1344 Dihedral : 3.652 17.869 1016 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.69 % Allowed : 22.65 % Favored : 75.66 % 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: 1.38 (0.29), residues: 944 helix: 3.13 (0.27), residues: 348 sheet: -0.08 (0.26), residues: 388 loop : -0.87 (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 C 43 PHE 0.005 0.001 PHE A 98 TYR 0.005 0.000 TYR A 171 ARG 0.004 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.02530 ( 513) hydrogen bonds : angle 4.80079 ( 1488) covalent geometry : bond 0.00220 ( 7760) covalent geometry : angle 0.70652 (10520) *********************** 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 112 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.301 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: B 122 GLN cc_start: 0.9533 (mt0) cc_final: 0.9158 (tm-30) REVERT: A 64 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8895 (tm-30) REVERT: G 122 GLN cc_start: 0.9538 (mt0) cc_final: 0.9154 (tm-30) REVERT: I 56 MET cc_start: 0.8894 (tpp) cc_final: 0.8295 (tpp) REVERT: F 64 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8867 (tm-30) outliers start: 14 outliers final: 13 residues processed: 102 average time/residue: 0.3386 time to fit residues: 49.7478 Evaluate side-chains 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.062334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.053237 restraints weight = 141022.164| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.78 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2929 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= 0.104 Angle : 0.706 26.454 10520 Z= 0.334 Chirality : 0.059 0.470 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.615 18.250 1016 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.05 % Allowed : 22.65 % 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: 1.43 (0.29), residues: 944 helix: 3.17 (0.27), residues: 348 sheet: -0.07 (0.26), residues: 388 loop : -0.82 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP E 41 HIS 0.002 0.001 HIS C 43 PHE 0.003 0.001 PHE I 48 TYR 0.004 0.000 TYR A 171 ARG 0.001 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02466 ( 513) hydrogen bonds : angle 4.71054 ( 1488) covalent geometry : bond 0.00225 ( 7760) covalent geometry : angle 0.70583 (10520) *********************** 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 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.218 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: A 64 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8826 (tm-30) REVERT: I 56 MET cc_start: 0.8872 (tpp) cc_final: 0.8134 (tpp) REVERT: F 64 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8832 (tm-30) outliers start: 17 outliers final: 15 residues processed: 100 average time/residue: 0.3288 time to fit residues: 47.3506 Evaluate side-chains 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 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 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 68 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 0.0980 chunk 78 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3673 r_free = 0.3673 target = 0.061355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052443 restraints weight = 141783.444| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.57 r_work: 0.3251 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3068 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= 0.129 Angle : 0.715 26.437 10520 Z= 0.336 Chirality : 0.059 0.467 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.589 18.739 1016 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.69 % Allowed : 22.77 % 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 (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: 1.45 (0.29), residues: 944 helix: 3.19 (0.27), residues: 348 sheet: -0.06 (0.26), residues: 388 loop : -0.82 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 41 HIS 0.002 0.001 HIS F 102 PHE 0.005 0.001 PHE E 35 TYR 0.004 0.000 TYR A 171 ARG 0.001 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.02451 ( 513) hydrogen bonds : angle 4.63868 ( 1488) covalent geometry : bond 0.00272 ( 7760) covalent geometry : angle 0.71485 (10520) *********************** 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 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.343 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: C 40 MET cc_start: 0.9036 (mmt) cc_final: 0.8788 (mmt) REVERT: A 64 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8885 (tm-30) REVERT: H 40 MET cc_start: 0.9057 (mmt) cc_final: 0.8792 (mmt) REVERT: I 56 MET cc_start: 0.8956 (tpp) cc_final: 0.8386 (tpp) REVERT: F 64 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8884 (tm-30) outliers start: 14 outliers final: 14 residues processed: 98 average time/residue: 0.3415 time to fit residues: 48.3161 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 : 1.227 ------------------------------------------------------------------------------- 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 233 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 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 20 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 250 GLN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.075884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.066163 restraints weight = 177482.338| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.50 r_work: 0.3190 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3143 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= 0.156 Angle : 0.721 26.262 10520 Z= 0.342 Chirality : 0.059 0.467 1188 Planarity : 0.003 0.033 1344 Dihedral : 3.612 18.682 1016 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.05 % Allowed : 22.41 % 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 (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: 1.46 (0.29), residues: 944 helix: 3.16 (0.27), residues: 348 sheet: -0.02 (0.27), residues: 388 loop : -0.81 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 41 HIS 0.003 0.001 HIS F 102 PHE 0.004 0.001 PHE F 126 TYR 0.012 0.001 TYR A 232 ARG 0.001 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02502 ( 513) hydrogen bonds : angle 4.61904 ( 1488) covalent geometry : bond 0.00322 ( 7760) covalent geometry : angle 0.72065 (10520) ********************** 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 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.278 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: B 126 MET cc_start: 0.9404 (tpp) cc_final: 0.8927 (tpp) REVERT: A 64 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8868 (tm-30) REVERT: G 126 MET cc_start: 0.9411 (tpp) cc_final: 0.9205 (tpp) REVERT: I 56 MET cc_start: 0.8981 (tpp) cc_final: 0.8394 (tpp) REVERT: F 64 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8882 (tm-30) outliers start: 17 outliers final: 15 residues processed: 100 average time/residue: 0.3434 time to fit residues: 49.7559 Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 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 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: 40.0000 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 36 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.061794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.052834 restraints weight = 139162.388| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.67 r_work: 0.3254 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3217 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= 0.111 Angle : 0.716 26.539 10520 Z= 0.337 Chirality : 0.060 0.465 1188 Planarity : 0.003 0.032 1344 Dihedral : 3.572 18.395 1016 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.81 % Allowed : 22.53 % Favored : 75.66 % 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: 1.49 (0.29), residues: 944 helix: 3.16 (0.27), residues: 348 sheet: 0.00 (0.27), residues: 388 loop : -0.75 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 41 HIS 0.002 0.001 HIS H 43 PHE 0.006 0.001 PHE A 98 TYR 0.004 0.000 TYR A 171 ARG 0.001 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.02436 ( 513) hydrogen bonds : angle 4.54488 ( 1488) covalent geometry : bond 0.00243 ( 7760) covalent geometry : angle 0.71605 (10520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6740.87 seconds wall clock time: 116 minutes 22.51 seconds (6982.51 seconds total)