Starting phenix.real_space_refine on Tue Feb 11 18:42:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zl4_14777/02_2025/7zl4_14777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zl4_14777/02_2025/7zl4_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_14777/02_2025/7zl4_14777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zl4_14777/02_2025/7zl4_14777.map" model { file = "/net/cci-nas-00/data/ceres_data/7zl4_14777/02_2025/7zl4_14777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zl4_14777/02_2025/7zl4_14777.cif" } resolution = 3.45 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= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.01, per 1000 atoms: 0.75 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: 2.11 Conformation dependent library (CDL) restraints added in 753.2 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: 0.70 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: 2.40 Time building geometry restraints manager: 2.27 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: 0.090 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.980 Find NCS groups from input model: 0.180 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- 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 3434 Z= 0.461 Angle : 1.391 6.722 4695 Z= 0.906 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 (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: -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 TRP 0.002 0.000 TRP B 42 PHE 0.015 0.003 PHE B 116 TYR 0.010 0.002 TYR B 108 ARG 0.001 0.000 ARG A 83 *********************** 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 : 0.557 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: 0.6918 (ttt180) cc_final: 0.6533 (ttt180) REVERT: A 129 PHE cc_start: 0.7924 (m-80) cc_final: 0.7647 (m-80) REVERT: B 5 GLN cc_start: 0.7947 (mt0) cc_final: 0.7535 (mt0) REVERT: B 150 LEU cc_start: 0.8963 (mt) cc_final: 0.8725 (tp) REVERT: C 9 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7864 (mtpp) REVERT: C 24 GLU cc_start: 0.7548 (tt0) cc_final: 0.7203 (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: 0.8062 (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: 0.3380 time to fit residues: 56.9970 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 : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.143862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115905 restraints weight = 13446.484| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.18 r_work: 0.3507 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3434 Z= 0.208 Angle : 0.576 6.794 4695 Z= 0.315 Chirality : 0.050 0.142 573 Planarity : 0.004 0.030 623 Dihedral : 4.426 15.308 488 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.91 % Allowed : 16.39 % 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 (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: -3.23 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.71 (0.41), residues: 151 loop : -2.52 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 PHE 0.015 0.001 PHE C 116 TYR 0.012 0.002 TYR A 108 ARG 0.002 0.001 ARG C 104 *********************** 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 108 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.516 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: 0.6456 (tpt) cc_final: 0.5696 (mtt) REVERT: A 86 LYS cc_start: 0.8938 (tttm) cc_final: 0.8657 (mtpp) REVERT: A 90 SER cc_start: 0.8486 (p) cc_final: 0.8219 (p) REVERT: A 112 GLN cc_start: 0.8853 (mm110) cc_final: 0.8396 (mm110) REVERT: B 5 GLN cc_start: 0.7809 (mt0) cc_final: 0.7557 (mt0) REVERT: B 9 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7667 (mtpp) REVERT: B 140 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7861 (mmtp) REVERT: C 70 ASP cc_start: 0.7910 (t70) cc_final: 0.7702 (p0) REVERT: C 112 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7365 (mm-40) outliers start: 7 outliers final: 6 residues processed: 105 average time/residue: 0.2812 time to fit residues: 36.5875 Evaluate side-chains 94 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 31 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111837 restraints weight = 13300.607| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.28 r_work: 0.3427 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3434 Z= 0.187 Angle : 0.516 5.941 4695 Z= 0.279 Chirality : 0.048 0.137 573 Planarity : 0.004 0.061 623 Dihedral : 4.071 13.606 488 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.91 % Allowed : 17.21 % 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 (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: -2.90 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.47 (0.43), residues: 151 loop : -2.29 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 PHE 0.011 0.001 PHE C 116 TYR 0.008 0.001 TYR A 108 ARG 0.003 0.001 ARG A 104 *********************** 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 97 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6561 (tpt) cc_final: 0.5619 (mtt) REVERT: A 73 VAL cc_start: 0.9136 (t) cc_final: 0.8754 (t) REVERT: A 86 LYS cc_start: 0.8923 (tttm) cc_final: 0.8645 (mtpp) REVERT: A 90 SER cc_start: 0.8411 (p) cc_final: 0.8160 (p) REVERT: A 112 GLN cc_start: 0.8871 (mm110) cc_final: 0.8558 (mm-40) REVERT: B 5 GLN cc_start: 0.7775 (mt0) cc_final: 0.7513 (mt0) REVERT: B 9 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7865 (mtpp) REVERT: C 112 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7489 (mm-40) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.2523 time to fit residues: 30.5738 Evaluate side-chains 91 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 47 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.135501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105469 restraints weight = 13550.360| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.35 r_work: 0.3320 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3434 Z= 0.228 Angle : 0.517 6.524 4695 Z= 0.276 Chirality : 0.048 0.134 573 Planarity : 0.004 0.052 623 Dihedral : 4.034 13.154 488 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.28 % Allowed : 16.39 % 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 (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: -2.65 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.19 (0.48), residues: 134 loop : -2.15 (0.27), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 42 PHE 0.027 0.002 PHE A 116 TYR 0.012 0.002 TYR A 108 ARG 0.004 0.001 ARG C 83 *********************** 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 103 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6851 (tpt) cc_final: 0.5951 (mtt) REVERT: A 42 TRP cc_start: 0.7702 (p90) cc_final: 0.7154 (p90) REVERT: A 112 GLN cc_start: 0.8906 (mm110) cc_final: 0.8666 (mm-40) REVERT: B 9 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8168 (mtpp) REVERT: B 44 ASN cc_start: 0.8286 (m110) cc_final: 0.7547 (m-40) REVERT: C 27 MET cc_start: 0.7528 (tpt) cc_final: 0.6998 (tpt) REVERT: C 107 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8055 (tt) REVERT: C 112 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7551 (mm-40) outliers start: 12 outliers final: 9 residues processed: 96 average time/residue: 0.2702 time to fit residues: 32.4675 Evaluate side-chains 90 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain C residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.130022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.098650 restraints weight = 13613.746| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.50 r_work: 0.3292 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3434 Z= 0.257 Angle : 0.512 6.207 4695 Z= 0.275 Chirality : 0.048 0.142 573 Planarity : 0.004 0.049 623 Dihedral : 4.032 13.202 488 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.28 % Allowed : 16.39 % 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 (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: -2.68 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.46 (0.42), residues: 156 loop : -2.05 (0.28), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 42 PHE 0.011 0.002 PHE A 116 TYR 0.009 0.002 TYR C 108 ARG 0.004 0.001 ARG C 83 *********************** 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 102 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7050 (tpt) cc_final: 0.6221 (mtt) REVERT: A 42 TRP cc_start: 0.7677 (p90) cc_final: 0.7151 (p90) REVERT: A 112 GLN cc_start: 0.8873 (mm110) cc_final: 0.8419 (tp40) REVERT: B 44 ASN cc_start: 0.7921 (m110) cc_final: 0.7200 (m110) REVERT: C 27 MET cc_start: 0.7411 (tpt) cc_final: 0.6881 (tpt) REVERT: C 33 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 62 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7365 (p) REVERT: C 112 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7526 (mm-40) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.2748 time to fit residues: 32.5174 Evaluate side-chains 96 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 B residue 145 TYR 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 62 THR Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.131902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102334 restraints weight = 13427.949| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.28 r_work: 0.3305 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3434 Z= 0.207 Angle : 0.497 6.105 4695 Z= 0.267 Chirality : 0.047 0.136 573 Planarity : 0.004 0.054 623 Dihedral : 3.982 14.678 488 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.55 % Allowed : 18.03 % 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 (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: -2.62 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.44 (0.42), residues: 156 loop : -1.99 (0.28), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 42 PHE 0.012 0.001 PHE A 116 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG B 104 *********************** 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 102 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7289 (tpt) cc_final: 0.6320 (mtt) REVERT: A 42 TRP cc_start: 0.7626 (p90) cc_final: 0.7139 (p90) REVERT: A 112 GLN cc_start: 0.8884 (mm110) cc_final: 0.8458 (tp40) REVERT: B 44 ASN cc_start: 0.7929 (m110) cc_final: 0.7214 (m110) REVERT: C 62 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7423 (p) REVERT: C 112 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7649 (mm-40) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.2504 time to fit residues: 29.8791 Evaluate side-chains 96 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 B residue 145 TYR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.131944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100922 restraints weight = 13408.056| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.51 r_work: 0.3298 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3434 Z= 0.147 Angle : 0.487 5.750 4695 Z= 0.257 Chirality : 0.047 0.132 573 Planarity : 0.004 0.052 623 Dihedral : 3.780 12.565 488 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.91 % Allowed : 19.95 % 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 (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: -2.48 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.34 (0.42), residues: 156 loop : -1.90 (0.29), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 42 PHE 0.009 0.001 PHE C 116 TYR 0.006 0.001 TYR A 108 ARG 0.002 0.000 ARG C 104 *********************** 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 98 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7403 (tpt) cc_final: 0.6372 (mtt) REVERT: A 42 TRP cc_start: 0.7563 (p90) cc_final: 0.7064 (p90) REVERT: A 112 GLN cc_start: 0.8902 (mm110) cc_final: 0.8484 (tp40) REVERT: B 44 ASN cc_start: 0.7898 (m110) cc_final: 0.7171 (m110) REVERT: B 112 GLN cc_start: 0.8754 (tp40) cc_final: 0.8529 (mm-40) REVERT: B 150 LEU cc_start: 0.9010 (mt) cc_final: 0.8715 (mm) REVERT: C 112 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7656 (mm-40) REVERT: C 122 GLN cc_start: 0.6676 (tm-30) cc_final: 0.5816 (tm-30) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2681 time to fit residues: 31.7853 Evaluate side-chains 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102294 restraints weight = 13508.381| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.22 r_work: 0.3312 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3434 Z= 0.213 Angle : 0.488 5.935 4695 Z= 0.262 Chirality : 0.047 0.135 573 Planarity : 0.003 0.047 623 Dihedral : 3.882 12.875 488 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.73 % Allowed : 19.13 % 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 (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: -2.62 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.66 (0.39), residues: 171 loop : -1.83 (0.30), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 42 PHE 0.009 0.001 PHE A 116 TYR 0.008 0.001 TYR A 108 ARG 0.003 0.000 ARG C 83 *********************** 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 96 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7512 (tpt) cc_final: 0.6459 (mtt) REVERT: A 112 GLN cc_start: 0.8885 (mm110) cc_final: 0.8401 (tp40) REVERT: B 44 ASN cc_start: 0.7908 (m110) cc_final: 0.7197 (m110) REVERT: B 112 GLN cc_start: 0.8717 (tp40) cc_final: 0.8502 (mm-40) REVERT: B 150 LEU cc_start: 0.9048 (mt) cc_final: 0.8784 (mm) REVERT: C 27 MET cc_start: 0.7220 (tpt) cc_final: 0.6604 (tpt) REVERT: C 112 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7811 (mm-40) REVERT: C 122 GLN cc_start: 0.6441 (tm-30) cc_final: 0.5883 (tm-30) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.2529 time to fit residues: 28.9368 Evaluate side-chains 94 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 9 LYS 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 92 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.132290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102747 restraints weight = 13409.595| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.31 r_work: 0.3312 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3434 Z= 0.161 Angle : 0.490 5.702 4695 Z= 0.261 Chirality : 0.047 0.131 573 Planarity : 0.004 0.049 623 Dihedral : 3.770 12.610 488 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.91 % Allowed : 19.40 % 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 (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: -2.54 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.62 (0.40), residues: 171 loop : -1.75 (0.30), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 42 PHE 0.009 0.001 PHE C 116 TYR 0.006 0.001 TYR A 108 ARG 0.003 0.000 ARG C 83 *********************** 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 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7592 (tpt) cc_final: 0.6380 (mtt) REVERT: A 112 GLN cc_start: 0.8875 (mm110) cc_final: 0.8399 (tp40) REVERT: B 44 ASN cc_start: 0.7825 (m110) cc_final: 0.7139 (m110) REVERT: B 150 LEU cc_start: 0.8999 (mt) cc_final: 0.8766 (mm) REVERT: C 27 MET cc_start: 0.7298 (tpt) cc_final: 0.6717 (tpt) REVERT: C 112 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7677 (mm-40) REVERT: C 122 GLN cc_start: 0.6298 (tm-30) cc_final: 0.5863 (tm-30) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.2562 time to fit residues: 27.9510 Evaluate side-chains 88 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 9 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.129970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101761 restraints weight = 13636.016| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.15 r_work: 0.3252 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3434 Z= 0.205 Angle : 0.496 5.863 4695 Z= 0.266 Chirality : 0.047 0.137 573 Planarity : 0.003 0.046 623 Dihedral : 3.817 12.461 488 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.91 % Allowed : 19.13 % 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 (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: -2.45 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.61 (0.41), residues: 161 loop : -1.68 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 42 PHE 0.009 0.001 PHE C 116 TYR 0.008 0.001 TYR A 108 ARG 0.002 0.000 ARG B 104 ********************** 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 91 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7598 (tpt) cc_final: 0.6413 (mtt) REVERT: A 86 LYS cc_start: 0.8807 (tttp) cc_final: 0.8589 (tptp) REVERT: A 112 GLN cc_start: 0.8874 (mm110) cc_final: 0.8394 (tp40) REVERT: B 44 ASN cc_start: 0.7890 (m110) cc_final: 0.7230 (m110) REVERT: B 150 LEU cc_start: 0.9002 (mt) cc_final: 0.8771 (mm) REVERT: C 27 MET cc_start: 0.7308 (tpt) cc_final: 0.6657 (tpt) REVERT: C 112 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7743 (mm-40) REVERT: C 122 GLN cc_start: 0.6320 (tm-30) cc_final: 0.5881 (tm-30) outliers start: 7 outliers final: 7 residues processed: 85 average time/residue: 0.2568 time to fit residues: 27.8080 Evaluate side-chains 90 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 9 LYS 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 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.130495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102463 restraints weight = 13633.102| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.17 r_work: 0.3294 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3434 Z= 0.174 Angle : 0.495 5.694 4695 Z= 0.263 Chirality : 0.047 0.132 573 Planarity : 0.003 0.047 623 Dihedral : 3.758 12.405 488 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.19 % Allowed : 18.31 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.52 (0.41), residues: 161 loop : -1.64 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 42 PHE 0.009 0.001 PHE A 116 TYR 0.007 0.001 TYR A 108 ARG 0.003 0.001 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4143.67 seconds wall clock time: 73 minutes 41.79 seconds (4421.79 seconds total)