Starting phenix.real_space_refine on Tue Feb 11 14:16:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6m_41072/02_2025/8t6m_41072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6m_41072/02_2025/8t6m_41072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6m_41072/02_2025/8t6m_41072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6m_41072/02_2025/8t6m_41072.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6m_41072/02_2025/8t6m_41072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6m_41072/02_2025/8t6m_41072.cif" } resolution = 3.14 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= 0.012 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3733 2.51 5 N 1003 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5903 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 945 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1476 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "F" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 801 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 6.64, per 1000 atoms: 1.12 Number of scatterers: 5903 At special positions: 0 Unit cell: (75.24, 111.54, 106.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1145 8.00 N 1003 7.00 C 3733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS B 113 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 112 " distance=2.03 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 81 " distance=2.03 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: 1.45 Conformation dependent library (CDL) restraints added in 946.2 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 16 sheets defined 14.3% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.840A pdb=" N ILE A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.076A pdb=" N PHE C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'E' and resid 49 through 54 Processing helix chain 'E' and resid 56 through 86 removed outlier: 3.607A pdb=" N TRP E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'E' and resid 151 through 162 removed outlier: 3.649A pdb=" N GLN E 155 " --> pdb=" O HIS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 175 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 23 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.668A pdb=" N TRP B 54 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 68 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 52 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.584A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 109 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.584A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 109 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.625A pdb=" N GLN D 93 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 73 through 75 removed outlier: 6.881A pdb=" N TRP D 52 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR D 66 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP D 50 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR D 49 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS D 111 " --> pdb=" O TRP D 128 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP D 128 " --> pdb=" O CYS D 111 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS D 113 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR D 117 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE D 122 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 73 through 75 removed outlier: 6.881A pdb=" N TRP D 52 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR D 66 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP D 50 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR D 49 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 46 through 47 removed outlier: 5.256A pdb=" N GLN E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 28 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG E 114 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE E 124 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR E 118 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP E 122 " --> pdb=" O TYR E 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 9 through 12 removed outlier: 5.900A pdb=" N PHE F 63 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'F' and resid 37 through 38 276 hydrogen bonds defined for protein. 693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1875 1.33 - 1.45: 1265 1.45 - 1.57: 2883 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 6053 Sorted by residual: bond pdb=" C PRO D 56 " pdb=" O PRO D 56 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 3.99e+00 bond pdb=" CA ASN F 22 " pdb=" C ASN F 22 " ideal model delta sigma weight residual 1.524 1.500 0.023 1.26e-02 6.30e+03 3.44e+00 bond pdb=" CA ALA E 24 " pdb=" C ALA E 24 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.24e-02 6.50e+03 3.42e+00 bond pdb=" CA GLY E 26 " pdb=" C GLY E 26 " ideal model delta sigma weight residual 1.520 1.507 0.013 7.30e-03 1.88e+04 3.39e+00 bond pdb=" CA SER C 77 " pdb=" C SER C 77 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.30e-02 5.92e+03 3.35e+00 ... (remaining 6048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 6719 1.16 - 2.31: 1235 2.31 - 3.47: 205 3.47 - 4.62: 49 4.62 - 5.78: 14 Bond angle restraints: 8222 Sorted by residual: angle pdb=" C GLY E 56 " pdb=" N PRO E 57 " pdb=" CA PRO E 57 " ideal model delta sigma weight residual 119.05 124.51 -5.46 1.11e+00 8.12e-01 2.42e+01 angle pdb=" C ASP E 119 " pdb=" CA ASP E 119 " pdb=" CB ASP E 119 " ideal model delta sigma weight residual 117.23 111.46 5.77 1.36e+00 5.41e-01 1.80e+01 angle pdb=" O PRO D 56 " pdb=" C PRO D 56 " pdb=" N PRO D 57 " ideal model delta sigma weight residual 121.15 123.10 -1.95 4.70e-01 4.53e+00 1.72e+01 angle pdb=" C LEU A 71 " pdb=" CA LEU A 71 " pdb=" CB LEU A 71 " ideal model delta sigma weight residual 116.54 111.90 4.64 1.15e+00 7.56e-01 1.63e+01 angle pdb=" N SER C 89 " pdb=" CA SER C 89 " pdb=" C SER C 89 " ideal model delta sigma weight residual 108.60 114.10 -5.50 1.46e+00 4.69e-01 1.42e+01 ... (remaining 8217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 3280 16.70 - 33.40: 236 33.40 - 50.10: 46 50.10 - 66.80: 5 66.80 - 83.49: 4 Dihedral angle restraints: 3571 sinusoidal: 1419 harmonic: 2152 Sorted by residual: dihedral pdb=" CA SER C 31 " pdb=" C SER C 31 " pdb=" N PRO C 32 " pdb=" CA PRO C 32 " ideal model delta harmonic sigma weight residual 0.00 -28.90 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CB CYS F 26 " pdb=" SG CYS F 26 " pdb=" SG CYS F 81 " pdb=" CB CYS F 81 " ideal model delta sinusoidal sigma weight residual 93.00 139.09 -46.09 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA GLY D 118 " pdb=" C GLY D 118 " pdb=" N SER D 119 " pdb=" CA SER D 119 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 3568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 662 0.033 - 0.065: 137 0.065 - 0.097: 50 0.097 - 0.130: 25 0.130 - 0.162: 11 Chirality restraints: 885 Sorted by residual: chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE B 55 " pdb=" N ILE B 55 " pdb=" C ILE B 55 " pdb=" CB ILE B 55 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE A 45 " pdb=" N ILE A 45 " pdb=" C ILE A 45 " pdb=" CB ILE A 45 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 882 not shown) Planarity restraints: 1055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 72 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO F 73 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 73 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 73 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 24 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 25 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 90 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO F 91 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 91 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 91 " 0.017 5.00e-02 4.00e+02 ... (remaining 1052 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 966 2.76 - 3.30: 6297 3.30 - 3.83: 10895 3.83 - 4.37: 12918 4.37 - 4.90: 21971 Nonbonded interactions: 53047 Sorted by model distance: nonbonded pdb=" OD1 ASP B 107 " pdb=" N THR B 108 " model vdw 2.226 3.120 nonbonded pdb=" O CYS C 112 " pdb=" N GLY C 123 " model vdw 2.351 3.120 nonbonded pdb=" C ASP B 107 " pdb=" OD1 ASP B 107 " model vdw 2.389 3.270 nonbonded pdb=" OG SER C 84 " pdb=" O GLN E 87 " model vdw 2.446 3.040 nonbonded pdb=" O LYS E 68 " pdb=" OG SER E 71 " model vdw 2.447 3.040 ... (remaining 53042 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 8.250 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4908 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 0.033 6053 Z= 0.428 Angle : 0.959 5.777 8222 Z= 0.646 Chirality : 0.039 0.162 885 Planarity : 0.004 0.041 1055 Dihedral : 11.951 83.494 2180 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.61 % Allowed : 5.99 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.30), residues: 732 helix: 2.26 (0.54), residues: 75 sheet: 1.45 (0.31), residues: 303 loop : 0.17 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 133 HIS 0.005 0.001 HIS F 32 PHE 0.013 0.002 PHE A 95 TYR 0.015 0.002 TYR E 99 ARG 0.005 0.001 ARG E 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.665 Fit side-chains REVERT: B 141 VAL cc_start: 0.4614 (t) cc_final: 0.4409 (t) REVERT: C 109 SER cc_start: 0.6135 (m) cc_final: 0.5875 (t) REVERT: D 91 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6589 (tt0) REVERT: E 132 SER cc_start: 0.6453 (m) cc_final: 0.6138 (m) REVERT: E 138 MET cc_start: 0.3059 (mtt) cc_final: 0.2794 (tmm) REVERT: F 90 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6959 (pt0) outliers start: 17 outliers final: 2 residues processed: 177 average time/residue: 0.2019 time to fit residues: 45.1874 Evaluate side-chains 116 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain D residue 22 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 57 GLN D 19 GLN F 3 GLN F 22 ASN F 84 ASN G 4 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114144 restraints weight = 7268.159| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.24 r_work: 0.3246 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6053 Z= 0.341 Angle : 0.683 7.234 8222 Z= 0.367 Chirality : 0.047 0.189 885 Planarity : 0.005 0.036 1055 Dihedral : 6.609 60.433 823 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.53 % Allowed : 11.52 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.31), residues: 732 helix: 2.16 (0.55), residues: 75 sheet: 1.41 (0.32), residues: 302 loop : 0.22 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 52 HIS 0.009 0.002 HIS G 4 PHE 0.018 0.002 PHE C 91 TYR 0.018 0.002 TYR E 27 ARG 0.006 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: D 46 GLU cc_start: 0.7900 (tt0) cc_final: 0.7638 (tt0) REVERT: E 65 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7244 (mtm180) REVERT: E 138 MET cc_start: 0.5036 (mtt) cc_final: 0.4476 (tmm) REVERT: F 13 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.5289 (tpm170) REVERT: F 60 ASP cc_start: 0.7272 (m-30) cc_final: 0.6933 (t0) outliers start: 23 outliers final: 16 residues processed: 138 average time/residue: 0.1898 time to fit residues: 33.8304 Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN E 86 ASN G 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116489 restraints weight = 7346.577| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.21 r_work: 0.3268 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6053 Z= 0.207 Angle : 0.570 8.062 8222 Z= 0.305 Chirality : 0.043 0.195 885 Planarity : 0.004 0.031 1055 Dihedral : 5.575 58.234 820 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.53 % Allowed : 13.98 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.31), residues: 732 helix: 1.96 (0.55), residues: 75 sheet: 1.34 (0.32), residues: 299 loop : 0.06 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 133 HIS 0.005 0.001 HIS G 4 PHE 0.012 0.001 PHE A 95 TYR 0.014 0.002 TYR E 27 ARG 0.004 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.702 Fit side-chains REVERT: B 89 LYS cc_start: 0.8334 (tttp) cc_final: 0.8108 (tttt) REVERT: E 27 TYR cc_start: 0.8202 (m-80) cc_final: 0.7998 (m-80) REVERT: E 103 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7329 (m) REVERT: E 138 MET cc_start: 0.5114 (mtt) cc_final: 0.4358 (tmm) REVERT: F 84 ASN cc_start: 0.8460 (t0) cc_final: 0.8144 (m-40) outliers start: 23 outliers final: 12 residues processed: 125 average time/residue: 0.1856 time to fit residues: 30.4272 Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN E 86 ASN E 87 GLN G 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106231 restraints weight = 7585.964| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.46 r_work: 0.3124 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 6053 Z= 0.514 Angle : 0.707 11.305 8222 Z= 0.377 Chirality : 0.049 0.289 885 Planarity : 0.005 0.042 1055 Dihedral : 6.115 68.368 820 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.30 % Allowed : 13.67 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.57 (0.31), residues: 732 helix: 1.39 (0.58), residues: 75 sheet: 0.91 (0.31), residues: 312 loop : -0.31 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 133 HIS 0.008 0.003 HIS F 52 PHE 0.016 0.002 PHE A 95 TYR 0.017 0.003 TYR E 27 ARG 0.008 0.001 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: B 89 LYS cc_start: 0.8467 (tttp) cc_final: 0.8193 (tttt) REVERT: C 126 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8485 (t) REVERT: E 103 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7409 (m) REVERT: E 138 MET cc_start: 0.5537 (mtt) cc_final: 0.4759 (tmm) REVERT: F 84 ASN cc_start: 0.8376 (t0) cc_final: 0.7997 (t0) outliers start: 41 outliers final: 27 residues processed: 136 average time/residue: 0.1745 time to fit residues: 31.7854 Evaluate side-chains 136 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN E 87 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111470 restraints weight = 7402.842| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.37 r_work: 0.3205 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6053 Z= 0.240 Angle : 0.579 14.739 8222 Z= 0.307 Chirality : 0.044 0.280 885 Planarity : 0.004 0.038 1055 Dihedral : 5.588 61.561 820 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.76 % Allowed : 17.05 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.63 (0.31), residues: 732 helix: 1.48 (0.58), residues: 75 sheet: 1.07 (0.32), residues: 297 loop : -0.33 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 51 HIS 0.006 0.001 HIS G 4 PHE 0.029 0.002 PHE F 71 TYR 0.028 0.002 TYR E 59 ARG 0.008 0.001 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.660 Fit side-chains REVERT: A 93 THR cc_start: 0.8671 (p) cc_final: 0.8204 (t) REVERT: B 89 LYS cc_start: 0.8423 (tttp) cc_final: 0.8182 (tttt) REVERT: C 126 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8294 (t) REVERT: E 108 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8113 (ptt180) REVERT: E 138 MET cc_start: 0.5125 (mtt) cc_final: 0.4378 (tmm) REVERT: E 158 VAL cc_start: 0.7755 (t) cc_final: 0.7499 (m) REVERT: F 84 ASN cc_start: 0.8357 (t0) cc_final: 0.8050 (t0) outliers start: 18 outliers final: 15 residues processed: 119 average time/residue: 0.1760 time to fit residues: 28.1050 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN E 180 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112094 restraints weight = 7370.881| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.17 r_work: 0.3208 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 6053 Z= 0.265 Angle : 0.573 12.460 8222 Z= 0.304 Chirality : 0.044 0.258 885 Planarity : 0.004 0.038 1055 Dihedral : 5.428 59.751 820 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.22 % Allowed : 15.51 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.55 (0.31), residues: 732 helix: 1.56 (0.58), residues: 75 sheet: 0.97 (0.31), residues: 298 loop : -0.38 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.005 0.001 HIS G 4 PHE 0.020 0.002 PHE F 71 TYR 0.015 0.002 TYR E 27 ARG 0.004 0.000 ARG E 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.645 Fit side-chains REVERT: A 93 THR cc_start: 0.8722 (p) cc_final: 0.8284 (t) REVERT: B 89 LYS cc_start: 0.8330 (tttp) cc_final: 0.8108 (tttt) REVERT: B 93 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: C 126 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8280 (t) REVERT: D 99 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8431 (mtpp) REVERT: E 138 MET cc_start: 0.5247 (mtt) cc_final: 0.4427 (tmm) REVERT: E 158 VAL cc_start: 0.7771 (t) cc_final: 0.7533 (m) REVERT: E 178 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7109 (m) REVERT: F 7 LYS cc_start: 0.8017 (ttmm) cc_final: 0.7639 (mttp) REVERT: F 84 ASN cc_start: 0.8373 (t0) cc_final: 0.8052 (t0) outliers start: 34 outliers final: 22 residues processed: 122 average time/residue: 0.1692 time to fit residues: 27.4326 Evaluate side-chains 127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.0020 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN G 4 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114117 restraints weight = 7414.275| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.38 r_work: 0.3248 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6053 Z= 0.187 Angle : 0.538 15.285 8222 Z= 0.284 Chirality : 0.042 0.251 885 Planarity : 0.004 0.038 1055 Dihedral : 5.113 53.282 820 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.07 % Allowed : 17.51 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.64 (0.31), residues: 732 helix: 1.76 (0.59), residues: 75 sheet: 1.03 (0.31), residues: 301 loop : -0.37 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 51 HIS 0.005 0.001 HIS G 4 PHE 0.014 0.001 PHE F 71 TYR 0.016 0.001 TYR E 27 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.670 Fit side-chains REVERT: A 89 SER cc_start: 0.8158 (t) cc_final: 0.7850 (p) REVERT: A 93 THR cc_start: 0.8733 (p) cc_final: 0.8318 (t) REVERT: B 89 LYS cc_start: 0.8310 (tttp) cc_final: 0.8107 (tttt) REVERT: B 93 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7262 (mp10) REVERT: C 126 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8165 (t) REVERT: D 99 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8418 (mtpp) REVERT: E 138 MET cc_start: 0.5066 (mtt) cc_final: 0.4189 (tmm) REVERT: E 158 VAL cc_start: 0.7795 (t) cc_final: 0.7565 (m) REVERT: E 178 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.7099 (m) REVERT: F 1 MET cc_start: 0.6600 (mpp) cc_final: 0.4411 (tpp) REVERT: F 7 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7511 (mttp) REVERT: F 84 ASN cc_start: 0.8338 (t0) cc_final: 0.8055 (t0) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.1818 time to fit residues: 27.5858 Evaluate side-chains 119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110262 restraints weight = 7356.216| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.36 r_work: 0.3191 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 6053 Z= 0.298 Angle : 0.586 15.732 8222 Z= 0.310 Chirality : 0.044 0.257 885 Planarity : 0.005 0.043 1055 Dihedral : 5.348 59.097 820 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.07 % Allowed : 18.13 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.48 (0.31), residues: 732 helix: 1.58 (0.58), residues: 75 sheet: 0.86 (0.31), residues: 302 loop : -0.39 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 PHE 0.012 0.002 PHE A 95 TYR 0.017 0.002 TYR E 27 ARG 0.004 0.001 ARG E 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.693 Fit side-chains REVERT: A 26 ILE cc_start: 0.8013 (mm) cc_final: 0.7731 (mm) REVERT: A 93 THR cc_start: 0.8754 (p) cc_final: 0.8360 (t) REVERT: B 89 LYS cc_start: 0.8399 (tttp) cc_final: 0.8179 (tttt) REVERT: C 117 ASP cc_start: 0.8748 (t70) cc_final: 0.8372 (t0) REVERT: C 126 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8310 (t) REVERT: D 93 GLN cc_start: 0.8453 (mt0) cc_final: 0.8149 (mm-40) REVERT: D 99 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8433 (mtpp) REVERT: E 138 MET cc_start: 0.5295 (mtt) cc_final: 0.4503 (tmm) REVERT: E 158 VAL cc_start: 0.7811 (t) cc_final: 0.7570 (m) REVERT: F 1 MET cc_start: 0.6655 (mpp) cc_final: 0.4442 (tpp) REVERT: F 7 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7668 (mttp) REVERT: F 84 ASN cc_start: 0.8369 (t0) cc_final: 0.8059 (t0) outliers start: 20 outliers final: 18 residues processed: 117 average time/residue: 0.1725 time to fit residues: 27.0996 Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111544 restraints weight = 7408.479| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.19 r_work: 0.3196 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6053 Z= 0.295 Angle : 0.592 15.535 8222 Z= 0.314 Chirality : 0.044 0.258 885 Planarity : 0.005 0.044 1055 Dihedral : 5.421 60.041 820 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.69 % Allowed : 18.13 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.33 (0.31), residues: 732 helix: 1.37 (0.57), residues: 75 sheet: 0.80 (0.31), residues: 299 loop : -0.50 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 PHE 0.011 0.001 PHE F 71 TYR 0.026 0.002 TYR E 59 ARG 0.005 0.001 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.714 Fit side-chains REVERT: A 93 THR cc_start: 0.8746 (p) cc_final: 0.8372 (t) REVERT: C 117 ASP cc_start: 0.8730 (t70) cc_final: 0.8353 (t0) REVERT: C 126 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8303 (t) REVERT: D 93 GLN cc_start: 0.8488 (mt0) cc_final: 0.8139 (mm-40) REVERT: D 99 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8462 (mtpp) REVERT: E 138 MET cc_start: 0.5268 (mtt) cc_final: 0.4458 (tmm) REVERT: E 158 VAL cc_start: 0.7794 (t) cc_final: 0.7547 (m) REVERT: F 7 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7641 (mttp) REVERT: F 84 ASN cc_start: 0.8370 (t0) cc_final: 0.8133 (t0) outliers start: 24 outliers final: 19 residues processed: 113 average time/residue: 0.1730 time to fit residues: 26.2690 Evaluate side-chains 120 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112912 restraints weight = 7363.650| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.18 r_work: 0.3218 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6053 Z= 0.236 Angle : 0.560 15.214 8222 Z= 0.298 Chirality : 0.043 0.252 885 Planarity : 0.004 0.047 1055 Dihedral : 5.238 57.001 820 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.76 % Allowed : 19.05 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.31 (0.31), residues: 732 helix: 1.51 (0.58), residues: 75 sheet: 0.69 (0.31), residues: 305 loop : -0.48 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 133 HIS 0.007 0.001 HIS G 4 PHE 0.011 0.001 PHE F 71 TYR 0.022 0.002 TYR E 59 ARG 0.004 0.000 ARG D 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.649 Fit side-chains REVERT: A 93 THR cc_start: 0.8738 (p) cc_final: 0.8376 (t) REVERT: C 117 ASP cc_start: 0.8703 (t70) cc_final: 0.8327 (t0) REVERT: C 126 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8242 (t) REVERT: D 93 GLN cc_start: 0.8410 (mt0) cc_final: 0.8135 (mm-40) REVERT: D 99 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8474 (mtpp) REVERT: E 138 MET cc_start: 0.5155 (mtt) cc_final: 0.4301 (tmm) REVERT: E 158 VAL cc_start: 0.7854 (t) cc_final: 0.7597 (m) REVERT: F 7 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7535 (mttp) REVERT: F 84 ASN cc_start: 0.8320 (t0) cc_final: 0.7997 (t0) outliers start: 18 outliers final: 17 residues processed: 111 average time/residue: 0.1691 time to fit residues: 25.1112 Evaluate side-chains 116 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 71 TRP Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain F residue 10 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 4 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109747 restraints weight = 7534.361| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.24 r_work: 0.3190 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6053 Z= 0.294 Angle : 0.586 15.394 8222 Z= 0.311 Chirality : 0.044 0.256 885 Planarity : 0.005 0.047 1055 Dihedral : 5.355 59.861 820 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.23 % Allowed : 19.05 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % 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: 0.22 (0.31), residues: 732 helix: 1.40 (0.58), residues: 75 sheet: 0.62 (0.31), residues: 305 loop : -0.50 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.006 0.001 HIS G 4 PHE 0.012 0.001 PHE A 95 TYR 0.025 0.002 TYR D 75 ARG 0.007 0.001 ARG D 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.46 seconds wall clock time: 69 minutes 14.39 seconds (4154.39 seconds total)