Starting phenix.real_space_refine on Thu Jul 24 17:20:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zl4_14777/07_2025/7zl4_14777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zl4_14777/07_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_14777/07_2025/7zl4_14777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zl4_14777/07_2025/7zl4_14777.map" model { file = "/net/cci-nas-00/data/ceres_data/7zl4_14777/07_2025/7zl4_14777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zl4_14777/07_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-5711/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: 4.02, per 1000 atoms: 0.60 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.32 Time building geometry restraints manager: 2.02 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.460 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:3.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3437 Z= 0.511 Angle : 1.395 6.722 4701 Z= 0.907 Chirality : 0.090 0.298 573 Planarity : 0.005 0.025 623 Dihedral : 16.420 84.834 1178 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.19022 ( 144) hydrogen bonds : angle 12.66802 ( 486) SS BOND : bond 0.01334 ( 3) SS BOND : angle 3.25782 ( 6) covalent geometry : bond 0.00703 ( 3434) covalent geometry : angle 1.39066 ( 4695) *********************** 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 : 0.491 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: 0.4036 time to fit residues: 69.6668 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 : 0.577 ------------------------------------------------------------------------------- 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 3437 Z= 0.144 Angle : 0.578 6.794 4701 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 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 144) hydrogen bonds : angle 8.19243 ( 486) SS BOND : bond 0.00136 ( 3) SS BOND : angle 1.33322 ( 6) covalent geometry : bond 0.00319 ( 3434) covalent geometry : angle 0.57606 ( 4695) *********************** 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 : 0.475 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: 0.2602 time to fit residues: 34.0621 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 : 0.452 ------------------------------------------------------------------------------- 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 3437 Z= 0.122 Angle : 0.517 5.847 4701 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 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 144) hydrogen bonds : angle 7.26720 ( 486) SS BOND : bond 0.00161 ( 3) SS BOND : angle 1.18076 ( 6) covalent geometry : bond 0.00257 ( 3434) covalent geometry : angle 0.51527 ( 4695) *********************** 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 : 0.510 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: 0.2629 time to fit residues: 31.7935 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 : 0.486 ------------------------------------------------------------------------------- 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 3437 Z= 0.208 Angle : 0.544 6.906 4701 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 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 144) hydrogen bonds : angle 6.99549 ( 486) SS BOND : bond 0.00105 ( 3) SS BOND : angle 1.15691 ( 6) covalent geometry : bond 0.00460 ( 3434) covalent geometry : angle 0.54320 ( 4695) *********************** 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 : 0.546 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: 0.2535 time to fit residues: 30.3031 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 : 0.531 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.132053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102930 restraints weight = 13598.330| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.22 r_work: 0.3294 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3437 Z= 0.152 Angle : 0.502 6.231 4701 Z= 0.269 Chirality : 0.048 0.140 573 Planarity : 0.004 0.054 623 Dihedral : 4.050 13.525 488 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.46 % Allowed : 18.85 % 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 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.54 (0.46), residues: 138 loop : -1.94 (0.27), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 42 PHE 0.010 0.001 PHE B 116 TYR 0.009 0.001 TYR C 108 ARG 0.003 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 144) hydrogen bonds : angle 6.75459 ( 486) SS BOND : bond 0.00098 ( 3) SS BOND : angle 1.08194 ( 6) covalent geometry : bond 0.00331 ( 3434) covalent geometry : angle 0.50049 ( 4695) *********************** 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 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7129 (tpt) cc_final: 0.6260 (mtt) REVERT: A 42 TRP cc_start: 0.7538 (p90) cc_final: 0.7088 (p90) REVERT: A 112 GLN cc_start: 0.8887 (mm110) cc_final: 0.8453 (tp40) REVERT: B 9 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8143 (mtpp) REVERT: B 150 LEU cc_start: 0.9073 (mt) cc_final: 0.8752 (mm) REVERT: C 27 MET cc_start: 0.7367 (tpt) cc_final: 0.6798 (tpt) REVERT: C 62 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7431 (p) REVERT: C 122 GLN cc_start: 0.6733 (tm-30) cc_final: 0.5903 (tm-30) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.2807 time to fit residues: 31.2007 Evaluate side-chains 85 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.130756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099569 restraints weight = 13418.656| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.47 r_work: 0.3261 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3437 Z= 0.120 Angle : 0.488 6.015 4701 Z= 0.260 Chirality : 0.047 0.135 573 Planarity : 0.003 0.047 623 Dihedral : 3.904 12.230 488 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.73 % Allowed : 20.22 % Favored : 77.05 % 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: -2.53 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.44 (0.45), residues: 138 loop : -1.89 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 42 PHE 0.009 0.001 PHE C 116 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 144) hydrogen bonds : angle 6.50301 ( 486) SS BOND : bond 0.00087 ( 3) SS BOND : angle 1.05025 ( 6) covalent geometry : bond 0.00266 ( 3434) covalent geometry : angle 0.48687 ( 4695) *********************** 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 96 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7167 (tpt) cc_final: 0.6231 (mtt) REVERT: A 42 TRP cc_start: 0.7683 (p90) cc_final: 0.7189 (p90) REVERT: A 112 GLN cc_start: 0.8899 (mm110) cc_final: 0.8683 (mm-40) REVERT: B 150 LEU cc_start: 0.9011 (mt) cc_final: 0.8674 (mm) REVERT: C 27 MET cc_start: 0.7315 (tpt) cc_final: 0.6764 (tpt) REVERT: C 62 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7351 (p) REVERT: C 122 GLN cc_start: 0.6821 (tm-30) cc_final: 0.6068 (tm-30) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.2507 time to fit residues: 28.7307 Evaluate side-chains 93 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.132751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103937 restraints weight = 13447.783| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.19 r_work: 0.3315 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3437 Z= 0.107 Angle : 0.475 5.792 4701 Z= 0.252 Chirality : 0.047 0.132 573 Planarity : 0.003 0.046 623 Dihedral : 3.768 12.818 488 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.19 % Allowed : 19.67 % 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: -2.56 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.60 (0.40), residues: 166 loop : -1.81 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 42 PHE 0.010 0.001 PHE C 116 TYR 0.006 0.001 TYR C 108 ARG 0.002 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.02686 ( 144) hydrogen bonds : angle 6.19972 ( 486) SS BOND : bond 0.00102 ( 3) SS BOND : angle 1.04923 ( 6) covalent geometry : bond 0.00242 ( 3434) covalent geometry : angle 0.47344 ( 4695) *********************** 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 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7377 (tpt) cc_final: 0.6295 (mtt) REVERT: A 42 TRP cc_start: 0.7487 (p90) cc_final: 0.7027 (p90) REVERT: A 112 GLN cc_start: 0.8879 (mm110) cc_final: 0.8401 (tp40) REVERT: B 49 GLU cc_start: 0.8015 (tt0) cc_final: 0.7799 (mt-10) REVERT: B 150 LEU cc_start: 0.9023 (mt) cc_final: 0.8723 (mm) REVERT: C 9 LYS cc_start: 0.8343 (mtpp) cc_final: 0.8110 (mtpt) REVERT: C 27 MET cc_start: 0.7312 (tpt) cc_final: 0.6813 (tpt) REVERT: C 62 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7431 (p) REVERT: C 122 GLN cc_start: 0.6618 (tm-30) cc_final: 0.6045 (tm-30) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.2493 time to fit residues: 27.6295 Evaluate side-chains 91 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 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 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=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: 2.9990 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.131591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102737 restraints weight = 13465.310| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.21 r_work: 0.3296 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3437 Z= 0.118 Angle : 0.479 5.708 4701 Z= 0.256 Chirality : 0.047 0.134 573 Planarity : 0.003 0.042 623 Dihedral : 3.761 12.141 488 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.46 % Allowed : 20.22 % 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: -2.52 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.57 (0.40), residues: 166 loop : -1.77 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 42 PHE 0.009 0.001 PHE C 116 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 144) hydrogen bonds : angle 6.16112 ( 486) SS BOND : bond 0.00071 ( 3) SS BOND : angle 1.00207 ( 6) covalent geometry : bond 0.00265 ( 3434) covalent geometry : angle 0.47799 ( 4695) *********************** 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 94 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7462 (tpt) cc_final: 0.6318 (mtt) REVERT: A 42 TRP cc_start: 0.7505 (p90) cc_final: 0.7034 (p90) REVERT: A 112 GLN cc_start: 0.8878 (mm110) cc_final: 0.8398 (tp40) REVERT: B 150 LEU cc_start: 0.9047 (mt) cc_final: 0.8796 (mm) REVERT: C 9 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8171 (mtpt) REVERT: C 27 MET cc_start: 0.7329 (tpt) cc_final: 0.6796 (tpt) REVERT: C 62 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7461 (p) REVERT: C 122 GLN cc_start: 0.6635 (tm-30) cc_final: 0.6085 (tm-30) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.2533 time to fit residues: 28.2961 Evaluate side-chains 92 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 62 THR Chi-restraints excluded: chain C residue 72 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: 10.0000 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.129614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100456 restraints weight = 13520.083| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.30 r_work: 0.3224 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3437 Z= 0.145 Angle : 0.492 5.917 4701 Z= 0.265 Chirality : 0.047 0.136 573 Planarity : 0.003 0.043 623 Dihedral : 3.867 11.914 488 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.01 % Allowed : 18.58 % 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: -2.54 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.61 (0.39), residues: 171 loop : -1.76 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 42 PHE 0.009 0.001 PHE C 116 TYR 0.009 0.001 TYR C 108 ARG 0.003 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.02796 ( 144) hydrogen bonds : angle 6.22580 ( 486) SS BOND : bond 0.00113 ( 3) SS BOND : angle 1.02906 ( 6) covalent geometry : bond 0.00323 ( 3434) covalent geometry : angle 0.49143 ( 4695) *********************** 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 95 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7593 (tpt) cc_final: 0.6382 (mtt) REVERT: A 112 GLN cc_start: 0.8887 (mm110) cc_final: 0.8465 (mm110) REVERT: B 150 LEU cc_start: 0.8991 (mt) cc_final: 0.8740 (mm) REVERT: C 9 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8163 (mtpt) REVERT: C 27 MET cc_start: 0.7361 (tpt) cc_final: 0.6731 (tpt) REVERT: C 62 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7444 (p) REVERT: C 122 GLN cc_start: 0.6576 (tm-30) cc_final: 0.6160 (tm-30) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.3162 time to fit residues: 35.5565 Evaluate side-chains 91 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.129776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098885 restraints weight = 13712.670| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.49 r_work: 0.3240 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3437 Z= 0.116 Angle : 0.487 5.652 4701 Z= 0.261 Chirality : 0.047 0.133 573 Planarity : 0.003 0.042 623 Dihedral : 3.772 12.160 488 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.46 % Allowed : 18.85 % 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: -2.35 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.50 (0.41), residues: 161 loop : -1.64 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 42 PHE 0.008 0.001 PHE C 116 TYR 0.007 0.001 TYR A 108 ARG 0.004 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.02687 ( 144) hydrogen bonds : angle 6.04658 ( 486) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.99220 ( 6) covalent geometry : bond 0.00262 ( 3434) covalent geometry : angle 0.48645 ( 4695) ********************** 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: 9 poor density : 81 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7557 (tpt) cc_final: 0.6342 (mtt) REVERT: A 112 GLN cc_start: 0.8887 (mm110) cc_final: 0.8415 (tp40) REVERT: B 150 LEU cc_start: 0.8975 (mt) cc_final: 0.8726 (mm) REVERT: C 9 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8111 (mtpt) REVERT: C 27 MET cc_start: 0.7252 (tpt) cc_final: 0.6649 (tpt) REVERT: C 62 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7350 (p) REVERT: C 122 GLN cc_start: 0.6550 (tm-30) cc_final: 0.6179 (tm-30) REVERT: C 142 GLN cc_start: 0.8327 (mp10) cc_final: 0.8051 (tt0) outliers start: 9 outliers final: 8 residues processed: 85 average time/residue: 0.3911 time to fit residues: 43.2098 Evaluate side-chains 90 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.128721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099812 restraints weight = 13787.172| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.25 r_work: 0.3252 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3437 Z= 0.147 Angle : 0.496 5.938 4701 Z= 0.267 Chirality : 0.047 0.140 573 Planarity : 0.003 0.042 623 Dihedral : 3.850 12.014 488 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.73 % Allowed : 18.58 % 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: -2.33 (0.36), residues: 457 helix: None (None), residues: 0 sheet: -1.51 (0.41), residues: 161 loop : -1.60 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 42 PHE 0.009 0.001 PHE C 116 TYR 0.009 0.001 TYR C 108 ARG 0.003 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 144) hydrogen bonds : angle 6.16330 ( 486) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.99615 ( 6) covalent geometry : bond 0.00329 ( 3434) covalent geometry : angle 0.49514 ( 4695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5044.03 seconds wall clock time: 88 minutes 53.56 seconds (5333.56 seconds total)