Starting phenix.real_space_refine on Tue Mar 11 18:11:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zl4_14777/03_2025/7zl4_14777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zl4_14777/03_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_14777/03_2025/7zl4_14777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zl4_14777/03_2025/7zl4_14777.map" model { file = "/net/cci-nas-00/data/ceres_data/7zl4_14777/03_2025/7zl4_14777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zl4_14777/03_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-5624/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: 3.75, per 1000 atoms: 0.56 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: 1.82 Conformation dependent library (CDL) restraints added in 584.7 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: 0.73 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: 2.42 Time building geometry restraints manager: 2.18 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: 0.120 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.370 Find NCS groups from input model: 0.190 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- 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 : 0.497 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: 0.3308 time to fit residues: 56.1363 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 : 0.491 ------------------------------------------------------------------------------- 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: 2.9990 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 = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115911 restraints weight = 13446.484| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.18 r_work: 0.3482 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.517 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: 0.6455 (tpt) cc_final: 0.5696 (mtt) REVERT: A 86 LYS cc_start: 0.8945 (tttm) cc_final: 0.8664 (mtpp) REVERT: A 90 SER cc_start: 0.8495 (p) cc_final: 0.8229 (p) REVERT: A 112 GLN cc_start: 0.8851 (mm110) cc_final: 0.8394 (mm110) REVERT: B 5 GLN cc_start: 0.7807 (mt0) cc_final: 0.7556 (mt0) REVERT: B 9 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7665 (mtpp) REVERT: B 140 LYS cc_start: 0.8080 (mmtp) cc_final: 0.7859 (mmtp) REVERT: C 70 ASP cc_start: 0.7900 (t70) cc_final: 0.7693 (p0) REVERT: C 112 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7363 (mm-40) outliers start: 7 outliers final: 6 residues processed: 105 average time/residue: 0.2860 time to fit residues: 37.5045 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 : 0.546 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.142350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110157 restraints weight = 13388.868| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.57 r_work: 0.3416 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4258 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= 0.170 Angle : 0.515 5.847 4695 Z= 0.279 Chirality : 0.049 0.138 573 Planarity : 0.004 0.061 623 Dihedral : 4.055 14.891 488 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -2.88 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.44 (0.43), residues: 151 loop : -2.28 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 42 PHE 0.011 0.001 PHE C 116 TYR 0.008 0.001 TYR A 108 ARG 0.003 0.000 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 98 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.555 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: 0.6541 (tpt) cc_final: 0.5592 (mtt) REVERT: A 86 LYS cc_start: 0.8927 (tttm) cc_final: 0.8652 (mtpp) REVERT: A 90 SER cc_start: 0.8416 (p) cc_final: 0.8165 (p) REVERT: A 112 GLN cc_start: 0.8879 (mm110) cc_final: 0.8361 (mm110) REVERT: B 5 GLN cc_start: 0.7752 (mt0) cc_final: 0.7485 (mt0) REVERT: B 9 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7738 (mtpp) REVERT: C 112 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7449 (mm-40) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.2519 time to fit residues: 30.5100 Evaluate side-chains 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 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 = 0.127569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095556 restraints weight = 13925.341| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.58 r_work: 0.3238 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3434 Z= 0.307 Angle : 0.543 6.906 4695 Z= 0.292 Chirality : 0.049 0.142 573 Planarity : 0.004 0.056 623 Dihedral : 4.221 13.690 488 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.83 % Allowed : 15.57 % Favored : 80.60 % 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: -2.76 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.35 (0.47), residues: 134 loop : -2.19 (0.27), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 42 PHE 0.011 0.002 PHE B 116 TYR 0.012 0.002 TYR C 108 ARG 0.005 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 102 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.544 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: 0.6915 (tpt) cc_final: 0.5944 (mtt) REVERT: A 42 TRP cc_start: 0.7768 (p90) cc_final: 0.7171 (p90) REVERT: A 112 GLN cc_start: 0.8883 (mm110) cc_final: 0.8576 (mm-40) REVERT: B 9 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8116 (mtpp) REVERT: C 27 MET cc_start: 0.7275 (tpt) cc_final: 0.6683 (tpt) REVERT: C 33 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8327 (mp) REVERT: C 64 ASP cc_start: 0.7570 (m-30) cc_final: 0.7355 (m-30) REVERT: C 107 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7998 (tt) outliers start: 14 outliers final: 9 residues processed: 94 average time/residue: 0.2589 time to fit residues: 31.0971 Evaluate side-chains 89 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 8 VAL 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: 0.7980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.131535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102209 restraints weight = 13664.958| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.25 r_work: 0.3282 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5606 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= 0.237 Angle : 0.507 6.250 4695 Z= 0.273 Chirality : 0.048 0.142 573 Planarity : 0.004 0.054 623 Dihedral : 4.076 13.507 488 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.73 % Allowed : 18.85 % 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: -2.63 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.55 (0.46), residues: 138 loop : -1.94 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 42 PHE 0.009 0.001 PHE B 116 TYR 0.008 0.001 TYR C 108 ARG 0.003 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 95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7043 (tpt) cc_final: 0.6228 (mtt) REVERT: A 42 TRP cc_start: 0.7610 (p90) cc_final: 0.7094 (p90) REVERT: A 112 GLN cc_start: 0.8880 (mm110) cc_final: 0.8438 (tp40) REVERT: B 9 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8162 (mtpp) REVERT: C 27 MET cc_start: 0.7321 (tpt) cc_final: 0.6726 (tpt) REVERT: C 62 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7408 (p) REVERT: C 122 GLN cc_start: 0.6825 (tm-30) cc_final: 0.6014 (tm-30) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.2812 time to fit residues: 31.4502 Evaluate side-chains 88 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.129946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101087 restraints weight = 13452.984| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.19 r_work: 0.3252 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5939 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= 0.224 Angle : 0.500 6.206 4695 Z= 0.268 Chirality : 0.048 0.135 573 Planarity : 0.004 0.054 623 Dihedral : 4.003 12.200 488 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.01 % Allowed : 20.49 % Favored : 76.50 % 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: -1.57 (0.41), residues: 156 loop : -1.97 (0.28), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 42 PHE 0.010 0.001 PHE B 116 TYR 0.009 0.001 TYR C 108 ARG 0.003 0.001 ARG C 83 *********************** 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 95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7309 (tpt) cc_final: 0.6318 (mtt) REVERT: A 42 TRP cc_start: 0.7683 (p90) cc_final: 0.7096 (p90) REVERT: A 112 GLN cc_start: 0.8870 (mm110) cc_final: 0.8358 (tp40) REVERT: B 150 LEU cc_start: 0.9026 (mt) cc_final: 0.8698 (mm) REVERT: C 27 MET cc_start: 0.7329 (tpt) cc_final: 0.6788 (tpt) REVERT: C 62 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7409 (p) REVERT: C 122 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6149 (tm-30) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.2425 time to fit residues: 27.5434 Evaluate side-chains 93 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 D residue 9 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.130787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102757 restraints weight = 13409.865| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.02 r_work: 0.3237 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6244 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= 0.235 Angle : 0.504 6.127 4695 Z= 0.271 Chirality : 0.048 0.140 573 Planarity : 0.004 0.052 623 Dihedral : 3.999 11.586 488 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.55 % Allowed : 19.13 % Favored : 77.32 % 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: -2.67 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.60 (0.41), residues: 156 loop : -1.95 (0.29), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 42 PHE 0.009 0.001 PHE B 116 TYR 0.009 0.001 TYR C 108 ARG 0.002 0.000 ARG B 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 94 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7493 (tpt) cc_final: 0.6299 (mtt) REVERT: A 60 SER cc_start: 0.8446 (m) cc_final: 0.8241 (p) REVERT: A 112 GLN cc_start: 0.8903 (mm110) cc_final: 0.8401 (tp40) REVERT: A 122 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6556 (tm-30) REVERT: B 24 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 150 LEU cc_start: 0.9091 (mt) cc_final: 0.8796 (mm) REVERT: C 27 MET cc_start: 0.7380 (tpt) cc_final: 0.6817 (tpt) REVERT: C 33 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (mp) REVERT: C 62 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7445 (p) REVERT: C 122 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6589 (tm-30) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.2614 time to fit residues: 29.0876 Evaluate side-chains 93 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 8 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098876 restraints weight = 13536.984| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.45 r_work: 0.3274 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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= 0.152 Angle : 0.473 5.722 4695 Z= 0.253 Chirality : 0.047 0.132 573 Planarity : 0.003 0.047 623 Dihedral : 3.807 11.078 488 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.73 % Allowed : 19.40 % 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 (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 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.76 (0.40), residues: 166 loop : -1.80 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 42 PHE 0.009 0.001 PHE C 116 TYR 0.006 0.001 TYR C 108 ARG 0.002 0.001 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 98 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7520 (tpt) cc_final: 0.6314 (mtt) REVERT: A 112 GLN cc_start: 0.9037 (mm110) cc_final: 0.8444 (tp40) REVERT: A 122 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6459 (tm-30) REVERT: B 24 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7068 (mm-30) REVERT: B 112 GLN cc_start: 0.8718 (tp40) cc_final: 0.8517 (mm-40) REVERT: B 150 LEU cc_start: 0.9000 (mt) cc_final: 0.8727 (mm) REVERT: C 9 LYS cc_start: 0.8328 (mtpp) cc_final: 0.8079 (mtpt) REVERT: C 27 MET cc_start: 0.7235 (tpt) cc_final: 0.6681 (tpt) REVERT: C 62 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7309 (p) REVERT: C 122 GLN cc_start: 0.6746 (tm-30) cc_final: 0.6314 (tm-30) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.2398 time to fit residues: 28.9503 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 : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 62 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.127936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099328 restraints weight = 13725.187| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.21 r_work: 0.3249 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3434 Z= 0.229 Angle : 0.506 5.992 4695 Z= 0.268 Chirality : 0.048 0.138 573 Planarity : 0.003 0.047 623 Dihedral : 3.926 12.410 488 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.01 % Allowed : 18.31 % 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: -2.63 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.77 (0.39), residues: 171 loop : -1.75 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 42 PHE 0.009 0.001 PHE C 116 TYR 0.008 0.001 TYR C 108 ARG 0.002 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: 11 poor density : 81 time to evaluate : 0.564 Fit side-chains REVERT: A 27 MET cc_start: 0.7562 (tpt) cc_final: 0.6374 (mtt) REVERT: A 112 GLN cc_start: 0.9032 (mm110) cc_final: 0.8445 (tp40) REVERT: B 150 LEU cc_start: 0.8987 (mt) cc_final: 0.8725 (mm) REVERT: C 27 MET cc_start: 0.7333 (tpt) cc_final: 0.6724 (tpt) REVERT: C 62 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7473 (p) REVERT: C 122 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6259 (tm-30) REVERT: C 142 GLN cc_start: 0.8488 (mp10) cc_final: 0.8105 (tt0) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.2618 time to fit residues: 29.0796 Evaluate side-chains 89 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 60 SER 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 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=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: 0.5980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.121555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092087 restraints weight = 14747.315| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.45 r_work: 0.3197 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.6656 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= 0.238 Angle : 0.524 6.032 4695 Z= 0.281 Chirality : 0.048 0.136 573 Planarity : 0.004 0.048 623 Dihedral : 3.988 13.312 488 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.84 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 (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: -2.57 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.67 (0.39), residues: 171 loop : -1.75 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 42 PHE 0.008 0.001 PHE B 116 TYR 0.010 0.002 TYR A 108 ARG 0.004 0.001 ARG C 83 ********************** 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 90 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.7614 (tpt) cc_final: 0.6383 (mtt) REVERT: A 112 GLN cc_start: 0.9032 (mm110) cc_final: 0.8435 (tp40) REVERT: B 60 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8114 (p) REVERT: B 150 LEU cc_start: 0.8972 (mt) cc_final: 0.8692 (mm) REVERT: C 27 MET cc_start: 0.7352 (tpt) cc_final: 0.6696 (tpt) REVERT: C 62 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7432 (p) REVERT: C 122 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6394 (tm-30) REVERT: C 142 GLN cc_start: 0.8558 (mp10) cc_final: 0.8126 (tt0) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.2636 time to fit residues: 27.9494 Evaluate side-chains 88 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 107 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 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.123672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094561 restraints weight = 14580.087| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.35 r_work: 0.3229 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.6784 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= 0.235 Angle : 0.520 5.982 4695 Z= 0.279 Chirality : 0.048 0.137 573 Planarity : 0.004 0.047 623 Dihedral : 4.063 14.829 488 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.28 % Allowed : 18.58 % 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: -2.49 (0.36), residues: 457 helix: None (None), residues: 0 sheet: -1.71 (0.43), residues: 153 loop : -1.67 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 42 PHE 0.008 0.001 PHE B 116 TYR 0.008 0.001 TYR A 108 ARG 0.004 0.001 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4744.87 seconds wall clock time: 80 minutes 59.52 seconds (4859.52 seconds total)