Starting phenix.real_space_refine on Tue Mar 3 15:08:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zl4_14777/03_2026/7zl4_14777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zl4_14777/03_2026/7zl4_14777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zl4_14777/03_2026/7zl4_14777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zl4_14777/03_2026/7zl4_14777.map" model { file = "/net/cci-nas-00/data/ceres_data/7zl4_14777/03_2026/7zl4_14777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zl4_14777/03_2026/7zl4_14777.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 9 5.16 5 C 2088 2.51 5 N 582 2.21 5 O 708 1.98 5 H 3291 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6678 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2017 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2226 Classifications: {'peptide': 155} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "C" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2226 Classifications: {'peptide': 155} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 209 Classifications: {'peptide': 14} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 13} Time building chain proxies: 1.41, per 1000 atoms: 0.21 Number of scatterers: 6678 At special positions: 0 Unit cell: (59.5654, 68.6297, 103.592, 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 9 16.00 O 708 8.00 N 582 7.00 C 2088 6.00 H 3291 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 63 " distance=2.04 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 63 " distance=2.04 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 63 " distance=2.04 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: 0.60 Conformation dependent library (CDL) restraints added in 303.9 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 61.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 4.359A pdb=" N ILE A 59 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 9.023A pdb=" N THR B 3 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS A 29 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 5 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B 11 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 37 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 148 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N THR A 84 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 52 removed outlier: 9.023A pdb=" N THR B 3 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS A 29 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 5 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B 11 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 37 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 removed outlier: 4.359A pdb=" N ILE B 59 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 24 removed outlier: 9.013A pdb=" N THR C 3 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 29 " --> pdb=" O THR C 3 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN C 5 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 11 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS B 37 " --> pdb=" O ASN C 11 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 148 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR B 84 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 52 removed outlier: 9.013A pdb=" N THR C 3 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 29 " --> pdb=" O THR C 3 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN C 5 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 11 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS B 37 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 removed outlier: 4.359A pdb=" N ILE C 59 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 24 removed outlier: 9.000A pdb=" N THR D 3 " --> pdb=" O MET C 27 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C 29 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN D 5 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 11 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 37 " --> pdb=" O ASN D 11 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 148 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR C 84 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 50 through 52 removed outlier: 9.000A pdb=" N THR D 3 " --> pdb=" O MET C 27 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C 29 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN D 5 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 11 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 37 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 99 195 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 3291 1.02 - 1.22: 26 1.22 - 1.42: 1377 1.42 - 1.63: 2019 1.63 - 1.83: 12 Bond restraints: 6725 Sorted by residual: bond pdb=" ND2 ASN C 135 " pdb="HD22 ASN C 135 " ideal model delta sigma weight residual 0.860 0.992 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" ND2 ASN B 135 " pdb="HD22 ASN B 135 " ideal model delta sigma weight residual 0.860 0.992 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" ND2 ASN A 135 " pdb="HD22 ASN A 135 " ideal model delta sigma weight residual 0.860 0.992 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" ND2 ASN A 87 " pdb="HD22 ASN A 87 " ideal model delta sigma weight residual 0.860 0.982 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" ND2 ASN B 43 " pdb="HD21 ASN B 43 " ideal model delta sigma weight residual 0.860 0.982 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 6720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10292 1.62 - 3.24: 1461 3.24 - 4.86: 294 4.86 - 6.48: 36 6.48 - 8.10: 15 Bond angle restraints: 12098 Sorted by residual: angle pdb=" N THR B 81 " pdb=" CA THR B 81 " pdb=" C THR B 81 " ideal model delta sigma weight residual 113.38 117.89 -4.51 1.17e+00 7.31e-01 1.48e+01 angle pdb=" N THR C 81 " pdb=" CA THR C 81 " pdb=" C THR C 81 " ideal model delta sigma weight residual 113.38 117.88 -4.50 1.17e+00 7.31e-01 1.48e+01 angle pdb=" N THR A 81 " pdb=" CA THR A 81 " pdb=" C THR A 81 " ideal model delta sigma weight residual 113.38 117.81 -4.43 1.17e+00 7.31e-01 1.44e+01 angle pdb=" N ALA A 102 " pdb=" CA ALA A 102 " pdb=" C ALA A 102 " ideal model delta sigma weight residual 112.38 116.88 -4.50 1.22e+00 6.72e-01 1.36e+01 angle pdb=" N ALA B 102 " pdb=" CA ALA B 102 " pdb=" C ALA B 102 " ideal model delta sigma weight residual 112.38 116.86 -4.48 1.22e+00 6.72e-01 1.35e+01 ... (remaining 12093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2643 17.96 - 35.92: 332 35.92 - 53.89: 153 53.89 - 71.85: 54 71.85 - 89.81: 24 Dihedral angle restraints: 3206 sinusoidal: 1749 harmonic: 1457 Sorted by residual: dihedral pdb=" SG CYS A 16 " pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" CA CYS A 63 " ideal model delta sinusoidal sigma weight residual 79.00 16.81 62.19 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" SG CYS B 16 " pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" CA CYS B 63 " ideal model delta sinusoidal sigma weight residual 79.00 16.82 62.18 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" SG CYS C 16 " pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" CA CYS C 63 " ideal model delta sinusoidal sigma weight residual 79.00 16.84 62.16 1 2.00e+01 2.50e-03 1.28e+01 ... (remaining 3203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 342 0.060 - 0.119: 125 0.119 - 0.179: 59 0.179 - 0.238: 35 0.238 - 0.298: 12 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA ILE A 59 " pdb=" N ILE A 59 " pdb=" C ILE A 59 " pdb=" CB ILE A 59 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 570 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 96 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C TYR B 96 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR B 96 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 97 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 96 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C TYR A 96 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR A 96 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 97 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 96 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C TYR C 96 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR C 96 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN C 97 " 0.014 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 1313 2.30 - 2.88: 14984 2.88 - 3.45: 17694 3.45 - 4.03: 24435 4.03 - 4.60: 35931 Nonbonded interactions: 94357 Sorted by model distance: nonbonded pdb=" H SER A 52 " pdb=" O GLY A 57 " model vdw 1.727 2.450 nonbonded pdb=" H SER B 52 " pdb=" O GLY B 57 " model vdw 1.727 2.450 nonbonded pdb=" H SER C 52 " pdb=" O GLY C 57 " model vdw 1.727 2.450 nonbonded pdb=" HG2 LYS B 86 " pdb=" HZ1 LYS B 86 " model vdw 1.745 2.270 nonbonded pdb=" HG2 LYS C 86 " pdb=" HZ1 LYS C 86 " model vdw 1.745 2.270 ... (remaining 94352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 15 through 155) selection = (chain 'C' and resid 15 through 155) } 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.007 0.036 3437 Z= 0.511 Angle : 1.395 6.722 4701 Z= 0.907 Chirality : 0.090 0.298 573 Planarity : 0.005 0.025 623 Dihedral : 16.420 84.834 1178 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.30), residues: 457 helix: None (None), residues: 0 sheet: -1.90 (0.37), residues: 158 loop : -3.36 (0.24), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.010 0.002 TYR B 108 PHE 0.015 0.003 PHE B 116 TRP 0.002 0.000 TRP B 42 Details of bonding type rmsd covalent geometry : bond 0.00703 ( 3434) covalent geometry : angle 1.39066 ( 4695) SS BOND : bond 0.01334 ( 3) SS BOND : angle 3.25782 ( 6) hydrogen bonds : bond 0.19022 ( 144) hydrogen bonds : angle 12.66802 ( 486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.173 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 27 MET cc_start: 0.6380 (tpt) cc_final: 0.5619 (mtt) REVERT: A 100 ARG cc_start: 0.6919 (ttt180) cc_final: 0.6535 (ttt180) REVERT: A 129 PHE cc_start: 0.7924 (m-80) cc_final: 0.7646 (m-80) REVERT: B 5 GLN cc_start: 0.7947 (mt0) cc_final: 0.7535 (mt0) REVERT: C 9 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7865 (mtpp) REVERT: C 24 GLU cc_start: 0.7548 (tt0) cc_final: 0.7204 (tt0) REVERT: C 70 ASP cc_start: 0.7918 (t70) cc_final: 0.7384 (p0) REVERT: C 86 LYS cc_start: 0.8265 (tttm) cc_final: 0.8063 (ttmm) REVERT: C 112 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7330 (mm-40) REVERT: C 150 LEU cc_start: 0.8807 (mt) cc_final: 0.8600 (mt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1573 time to fit residues: 26.6209 Evaluate side-chains 94 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.143921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116064 restraints weight = 13488.796| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.19 r_work: 0.3474 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3437 Z= 0.144 Angle : 0.572 6.708 4701 Z= 0.313 Chirality : 0.050 0.148 573 Planarity : 0.004 0.029 623 Dihedral : 4.419 15.450 488 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.64 % Allowed : 16.67 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.66 (0.41), residues: 151 loop : -2.52 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.012 0.002 TYR A 108 PHE 0.015 0.001 PHE C 116 TRP 0.004 0.001 TRP C 42 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3434) covalent geometry : angle 0.57005 ( 4695) SS BOND : bond 0.00082 ( 3) SS BOND : angle 1.30905 ( 6) hydrogen bonds : bond 0.03705 ( 144) hydrogen bonds : angle 8.20344 ( 486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.174 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: A 27 MET cc_start: 0.6423 (tpt) cc_final: 0.5657 (mtt) REVERT: A 86 LYS cc_start: 0.8958 (tttm) cc_final: 0.8673 (mtpp) REVERT: A 90 SER cc_start: 0.8545 (p) cc_final: 0.8282 (p) REVERT: A 112 GLN cc_start: 0.8848 (mm110) cc_final: 0.8263 (tp40) REVERT: B 5 GLN cc_start: 0.7732 (mt0) cc_final: 0.7482 (mt0) REVERT: B 9 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7636 (mtpp) REVERT: B 140 LYS cc_start: 0.8039 (mmtp) cc_final: 0.7835 (mmtp) REVERT: C 24 GLU cc_start: 0.7690 (tt0) cc_final: 0.7389 (tt0) REVERT: C 70 ASP cc_start: 0.7941 (t70) cc_final: 0.7729 (p0) REVERT: C 112 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7300 (mm-40) outliers start: 6 outliers final: 6 residues processed: 104 average time/residue: 0.1337 time to fit residues: 17.3307 Evaluate side-chains 95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101240 restraints weight = 13970.579| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.28 r_work: 0.3251 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3437 Z= 0.267 Angle : 0.595 6.830 4701 Z= 0.327 Chirality : 0.051 0.141 573 Planarity : 0.005 0.064 623 Dihedral : 4.426 14.679 488 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.73 % Allowed : 16.39 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.66 (0.43), residues: 146 loop : -2.29 (0.28), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 83 TYR 0.013 0.003 TYR A 145 PHE 0.011 0.002 PHE B 116 TRP 0.003 0.001 TRP C 42 Details of bonding type rmsd covalent geometry : bond 0.00590 ( 3434) covalent geometry : angle 0.59438 ( 4695) SS BOND : bond 0.00108 ( 3) SS BOND : angle 1.15260 ( 6) hydrogen bonds : bond 0.03698 ( 144) hydrogen bonds : angle 7.62808 ( 486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.188 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: A 27 MET cc_start: 0.6775 (tpt) cc_final: 0.5834 (mtt) REVERT: A 42 TRP cc_start: 0.7734 (p90) cc_final: 0.7105 (p90) REVERT: A 86 LYS cc_start: 0.9066 (tttm) cc_final: 0.8747 (mtpp) REVERT: A 112 GLN cc_start: 0.8875 (mm110) cc_final: 0.8413 (tp40) REVERT: B 5 GLN cc_start: 0.7842 (mt0) cc_final: 0.7539 (mt0) REVERT: B 9 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8205 (mtpp) REVERT: C 27 MET cc_start: 0.7438 (tpt) cc_final: 0.6858 (tpt) REVERT: C 107 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8103 (tt) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.1214 time to fit residues: 13.6159 Evaluate side-chains 80 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103852 restraints weight = 13794.343| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.29 r_work: 0.3323 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3437 Z= 0.139 Angle : 0.511 6.217 4701 Z= 0.274 Chirality : 0.048 0.134 573 Planarity : 0.003 0.053 623 Dihedral : 4.051 13.172 488 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.55 % Allowed : 16.12 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.55 (0.46), residues: 136 loop : -2.03 (0.28), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.009 0.001 TYR C 108 PHE 0.010 0.001 PHE B 116 TRP 0.004 0.001 TRP C 42 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3434) covalent geometry : angle 0.50938 ( 4695) SS BOND : bond 0.00130 ( 3) SS BOND : angle 1.11069 ( 6) hydrogen bonds : bond 0.03012 ( 144) hydrogen bonds : angle 6.99106 ( 486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.176 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: A 27 MET cc_start: 0.6928 (tpt) cc_final: 0.5946 (mtt) REVERT: A 42 TRP cc_start: 0.7586 (p90) cc_final: 0.7198 (p90) REVERT: A 86 LYS cc_start: 0.9007 (tttm) cc_final: 0.8690 (mtpp) REVERT: A 112 GLN cc_start: 0.8858 (mm110) cc_final: 0.8410 (tp40) REVERT: B 5 GLN cc_start: 0.7866 (mt0) cc_final: 0.7633 (mm-40) REVERT: B 9 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8119 (mtpp) REVERT: C 62 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7331 (p) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.1281 time to fit residues: 14.8790 Evaluate side-chains 89 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093276 restraints weight = 14176.549| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.44 r_work: 0.3168 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3437 Z= 0.292 Angle : 0.599 7.129 4701 Z= 0.325 Chirality : 0.051 0.146 573 Planarity : 0.005 0.057 623 Dihedral : 4.600 14.963 488 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.10 % Allowed : 17.49 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.86 (0.40), residues: 166 loop : -2.06 (0.29), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 83 TYR 0.012 0.002 TYR A 108 PHE 0.013 0.002 PHE B 30 TRP 0.005 0.001 TRP A 42 Details of bonding type rmsd covalent geometry : bond 0.00647 ( 3434) covalent geometry : angle 0.59766 ( 4695) SS BOND : bond 0.00255 ( 3) SS BOND : angle 1.07386 ( 6) hydrogen bonds : bond 0.03613 ( 144) hydrogen bonds : angle 7.23950 ( 486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7469 (tpt) cc_final: 0.6281 (mtt) REVERT: B 9 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8250 (mtpp) REVERT: C 27 MET cc_start: 0.7327 (tpt) cc_final: 0.6705 (tpt) REVERT: C 62 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7347 (p) outliers start: 15 outliers final: 10 residues processed: 87 average time/residue: 0.1172 time to fit residues: 13.1628 Evaluate side-chains 86 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 8 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.128905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099911 restraints weight = 14071.502| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.17 r_work: 0.3228 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3437 Z= 0.116 Angle : 0.525 5.940 4701 Z= 0.282 Chirality : 0.048 0.136 573 Planarity : 0.004 0.050 623 Dihedral : 4.075 12.241 488 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.28 % Allowed : 18.85 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.53 (0.46), residues: 138 loop : -1.92 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 104 TYR 0.008 0.001 TYR A 108 PHE 0.019 0.001 PHE A 116 TRP 0.003 0.001 TRP C 42 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3434) covalent geometry : angle 0.52358 ( 4695) SS BOND : bond 0.00108 ( 3) SS BOND : angle 1.03659 ( 6) hydrogen bonds : bond 0.02868 ( 144) hydrogen bonds : angle 6.69155 ( 486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7510 (tpt) cc_final: 0.6398 (mtt) REVERT: A 86 LYS cc_start: 0.9040 (tttp) cc_final: 0.8628 (tptp) REVERT: A 112 GLN cc_start: 0.8838 (mm110) cc_final: 0.8382 (tp40) REVERT: B 49 GLU cc_start: 0.7927 (tt0) cc_final: 0.7705 (mt-10) REVERT: C 62 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7363 (p) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.1283 time to fit residues: 13.8837 Evaluate side-chains 87 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 0 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.127353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098584 restraints weight = 14145.912| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.15 r_work: 0.3261 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3437 Z= 0.137 Angle : 0.508 5.911 4701 Z= 0.272 Chirality : 0.047 0.135 573 Planarity : 0.004 0.055 623 Dihedral : 4.043 12.091 488 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.55 % Allowed : 18.31 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.57 (0.41), residues: 156 loop : -1.99 (0.29), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 83 TYR 0.009 0.001 TYR A 108 PHE 0.017 0.001 PHE A 116 TRP 0.002 0.001 TRP C 42 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3434) covalent geometry : angle 0.50752 ( 4695) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.97339 ( 6) hydrogen bonds : bond 0.02824 ( 144) hydrogen bonds : angle 6.58336 ( 486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7544 (tpt) cc_final: 0.6424 (mtt) REVERT: A 86 LYS cc_start: 0.9037 (tttp) cc_final: 0.8644 (tptp) REVERT: A 112 GLN cc_start: 0.8835 (mm110) cc_final: 0.8387 (tp40) REVERT: C 62 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7424 (p) outliers start: 13 outliers final: 11 residues processed: 84 average time/residue: 0.1222 time to fit residues: 13.1186 Evaluate side-chains 90 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 8 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.0010 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.128325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100173 restraints weight = 14099.825| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.12 r_work: 0.3238 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3437 Z= 0.121 Angle : 0.493 5.622 4701 Z= 0.262 Chirality : 0.047 0.135 573 Planarity : 0.004 0.054 623 Dihedral : 3.863 12.142 488 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.83 % Allowed : 17.49 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.78 (0.40), residues: 166 loop : -1.81 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.007 0.001 TYR C 108 PHE 0.019 0.001 PHE A 116 TRP 0.003 0.001 TRP B 42 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3434) covalent geometry : angle 0.49200 ( 4695) SS BOND : bond 0.00159 ( 3) SS BOND : angle 0.90261 ( 6) hydrogen bonds : bond 0.02739 ( 144) hydrogen bonds : angle 6.33866 ( 486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7554 (tpt) cc_final: 0.6417 (mtt) REVERT: A 86 LYS cc_start: 0.9046 (tttp) cc_final: 0.8659 (tptp) REVERT: A 112 GLN cc_start: 0.8852 (mm110) cc_final: 0.8401 (tp40) REVERT: C 27 MET cc_start: 0.7413 (tpt) cc_final: 0.6873 (tpt) REVERT: C 62 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7341 (p) outliers start: 14 outliers final: 13 residues processed: 88 average time/residue: 0.1308 time to fit residues: 14.5022 Evaluate side-chains 93 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096732 restraints weight = 14311.453| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.42 r_work: 0.3228 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3437 Z= 0.119 Angle : 0.496 5.515 4701 Z= 0.264 Chirality : 0.047 0.132 573 Planarity : 0.004 0.050 623 Dihedral : 3.843 11.996 488 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.28 % Allowed : 18.31 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.74 (0.40), residues: 166 loop : -1.79 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 80 TYR 0.007 0.001 TYR A 108 PHE 0.015 0.001 PHE A 116 TRP 0.001 0.000 TRP B 42 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3434) covalent geometry : angle 0.49578 ( 4695) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.88060 ( 6) hydrogen bonds : bond 0.02682 ( 144) hydrogen bonds : angle 6.25473 ( 486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7555 (tpt) cc_final: 0.6369 (mtt) REVERT: A 86 LYS cc_start: 0.9077 (tttp) cc_final: 0.8679 (tptp) REVERT: A 112 GLN cc_start: 0.8877 (mm110) cc_final: 0.8421 (tp40) REVERT: B 150 LEU cc_start: 0.8973 (mt) cc_final: 0.8626 (mm) REVERT: C 27 MET cc_start: 0.7335 (tpt) cc_final: 0.6776 (tpt) REVERT: C 62 THR cc_start: 0.7472 (OUTLIER) cc_final: 0.7232 (p) REVERT: C 142 GLN cc_start: 0.8554 (mp10) cc_final: 0.8161 (tt0) outliers start: 12 outliers final: 10 residues processed: 85 average time/residue: 0.1314 time to fit residues: 14.0403 Evaluate side-chains 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.0770 chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.127004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097407 restraints weight = 14169.353| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.37 r_work: 0.3245 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3437 Z= 0.104 Angle : 0.488 5.308 4701 Z= 0.259 Chirality : 0.047 0.130 573 Planarity : 0.003 0.052 623 Dihedral : 3.699 11.948 488 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.19 % Allowed : 19.13 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.69 (0.39), residues: 171 loop : -1.71 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 83 TYR 0.007 0.001 TYR B 96 PHE 0.017 0.001 PHE A 116 TRP 0.004 0.001 TRP B 42 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3434) covalent geometry : angle 0.48784 ( 4695) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.83508 ( 6) hydrogen bonds : bond 0.02607 ( 144) hydrogen bonds : angle 6.04035 ( 486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7609 (tpt) cc_final: 0.6396 (mtt) REVERT: A 86 LYS cc_start: 0.9044 (tttp) cc_final: 0.8659 (tptp) REVERT: A 112 GLN cc_start: 0.9019 (mm110) cc_final: 0.8431 (tp40) REVERT: B 150 LEU cc_start: 0.8986 (mt) cc_final: 0.8707 (mm) REVERT: C 27 MET cc_start: 0.7357 (tpt) cc_final: 0.6822 (tpt) REVERT: C 142 GLN cc_start: 0.8558 (mp10) cc_final: 0.8160 (tt0) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.1299 time to fit residues: 14.0354 Evaluate side-chains 88 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.125422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095042 restraints weight = 14283.164| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.43 r_work: 0.3197 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3437 Z= 0.157 Angle : 0.500 5.602 4701 Z= 0.268 Chirality : 0.047 0.137 573 Planarity : 0.003 0.049 623 Dihedral : 3.872 11.711 488 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.73 % Allowed : 18.31 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.71 (0.39), residues: 171 loop : -1.67 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 83 TYR 0.009 0.001 TYR C 108 PHE 0.013 0.001 PHE A 116 TRP 0.003 0.001 TRP C 42 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3434) covalent geometry : angle 0.49980 ( 4695) SS BOND : bond 0.00192 ( 3) SS BOND : angle 0.88044 ( 6) hydrogen bonds : bond 0.02747 ( 144) hydrogen bonds : angle 6.20618 ( 486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.41 seconds wall clock time: 39 minutes 59.67 seconds (2399.67 seconds total)