Starting phenix.real_space_refine on Thu Jun 5 07:01:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5m_37297/06_2025/8w5m_37297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5m_37297/06_2025/8w5m_37297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5m_37297/06_2025/8w5m_37297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5m_37297/06_2025/8w5m_37297.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5m_37297/06_2025/8w5m_37297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5m_37297/06_2025/8w5m_37297.cif" } resolution = 3.1 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= 0.005 sd= 0.078 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 15 5.16 5 C 3519 2.51 5 N 995 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5645 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "b" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Time building chain proxies: 3.64, per 1000 atoms: 0.64 Number of scatterers: 5645 At special positions: 0 Unit cell: (101.64, 109.56, 89.76, 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 15 16.00 O 1116 8.00 N 995 7.00 C 3519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 93 " 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: 1.20 Conformation dependent library (CDL) restraints added in 662.1 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 12.8% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'b' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG b 105 " --> pdb=" O THR b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 125 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing sheet with id=AA1, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'L' and resid 48 through 53 removed outlier: 6.584A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.842A pdb=" N LEU H 7 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU H 9 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER H 24 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 74 " --> pdb=" O PHE H 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 50 through 54 removed outlier: 6.874A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR H 53 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG H 42 " --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET H 96 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA H 95 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 117 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR A 7 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 21 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 9 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 19 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 34 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 86 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 84 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER b 95 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL b 84 " --> pdb=" O CYS b 74 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS b 74 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG b 86 " --> pdb=" O THR b 72 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL b 32 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL b 26 " --> pdb=" O VAL b 32 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER b 34 " --> pdb=" O ARG b 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU b 19 " --> pdb=" O GLY b 9 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY b 9 " --> pdb=" O LEU b 19 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU b 21 " --> pdb=" O THR b 7 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR b 7 " --> pdb=" O LEU b 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR B 7 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 21 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY B 9 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 19 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER B 34 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B 26 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 86 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 84 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 5.244A pdb=" N THR C 7 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 21 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 9 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 19 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 582 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: 1.21 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 958 1.29 - 1.42: 1378 1.42 - 1.55: 3372 1.55 - 1.68: 14 1.68 - 1.81: 18 Bond restraints: 5740 Sorted by residual: bond pdb=" C VAL A 6 " pdb=" O VAL A 6 " ideal model delta sigma weight residual 1.236 1.156 0.081 1.20e-02 6.94e+03 4.53e+01 bond pdb=" C LEU A 3 " pdb=" O LEU A 3 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.20e-02 6.94e+03 2.99e+01 bond pdb=" C THR A 5 " pdb=" O THR A 5 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.20e-02 6.94e+03 2.76e+01 bond pdb=" CB THR A 5 " pdb=" CG2 THR A 5 " ideal model delta sigma weight residual 1.521 1.377 0.144 3.30e-02 9.18e+02 1.90e+01 bond pdb=" CA THR A 5 " pdb=" CB THR A 5 " ideal model delta sigma weight residual 1.529 1.461 0.068 1.64e-02 3.72e+03 1.70e+01 ... (remaining 5735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 7509 2.20 - 4.39: 249 4.39 - 6.59: 35 6.59 - 8.79: 13 8.79 - 10.98: 7 Bond angle restraints: 7813 Sorted by residual: angle pdb=" C SER C 53 " pdb=" N GLN C 54 " pdb=" CA GLN C 54 " ideal model delta sigma weight residual 120.86 130.18 -9.32 1.60e+00 3.91e-01 3.39e+01 angle pdb=" C SER b 53 " pdb=" N GLN b 54 " pdb=" CA GLN b 54 " ideal model delta sigma weight residual 120.86 130.16 -9.30 1.60e+00 3.91e-01 3.38e+01 angle pdb=" C SER B 53 " pdb=" N GLN B 54 " pdb=" CA GLN B 54 " ideal model delta sigma weight residual 120.86 130.15 -9.29 1.60e+00 3.91e-01 3.37e+01 angle pdb=" C SER A 53 " pdb=" N GLN A 54 " pdb=" CA GLN A 54 " ideal model delta sigma weight residual 120.86 130.13 -9.27 1.60e+00 3.91e-01 3.36e+01 angle pdb=" N VAL A 6 " pdb=" CA VAL A 6 " pdb=" CB VAL A 6 " ideal model delta sigma weight residual 111.83 105.69 6.14 1.23e+00 6.61e-01 2.49e+01 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 3316 14.03 - 28.06: 123 28.06 - 42.09: 29 42.09 - 56.12: 0 56.12 - 70.15: 4 Dihedral angle restraints: 3472 sinusoidal: 1315 harmonic: 2157 Sorted by residual: dihedral pdb=" CA GLY L 18 " pdb=" C GLY L 18 " pdb=" N GLU L 19 " pdb=" CA GLU L 19 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA ASP H 65 " pdb=" C ASP H 65 " pdb=" N THR H 66 " pdb=" CA THR H 66 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA CYS H 99 " pdb=" C CYS H 99 " pdb=" N ALA H 100 " pdb=" CA ALA H 100 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 3469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 599 0.050 - 0.101: 217 0.101 - 0.151: 74 0.151 - 0.201: 20 0.201 - 0.251: 11 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU b 128 " pdb=" CB LEU b 128 " pdb=" CD1 LEU b 128 " pdb=" CD2 LEU b 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU C 128 " pdb=" CB LEU C 128 " pdb=" CD1 LEU C 128 " pdb=" CD2 LEU C 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 918 not shown) Planarity restraints: 1021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 18 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C GLY L 18 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY L 18 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU L 19 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 67 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C VAL H 67 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL H 67 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS H 68 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL b 41 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO b 42 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO b 42 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO b 42 " 0.033 5.00e-02 4.00e+02 ... (remaining 1018 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1364 2.80 - 3.32: 4481 3.32 - 3.85: 8661 3.85 - 4.37: 9553 4.37 - 4.90: 17345 Nonbonded interactions: 41404 Sorted by model distance: nonbonded pdb=" N ALA A 1 " pdb=" OD2 ASP b 123 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR H 72 " pdb=" O GLN H 85 " model vdw 2.329 3.040 nonbonded pdb=" O ASP H 105 " pdb=" OH TYR H 109 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN B 87 " pdb=" OH TYR B 89 " model vdw 2.402 3.040 nonbonded pdb=" OE1 GLN A 87 " pdb=" OH TYR A 89 " model vdw 2.402 3.040 ... (remaining 41399 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 1 through 131) selection = chain 'C' selection = (chain 'b' and resid 1 through 131) } 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: 0.370 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 15.830 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.006 0.144 5741 Z= 0.309 Angle : 0.981 10.984 7815 Z= 0.546 Chirality : 0.063 0.251 921 Planarity : 0.008 0.061 1021 Dihedral : 8.719 70.155 2081 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.45 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.59 (0.26), residues: 739 helix: -2.05 (0.44), residues: 92 sheet: -1.48 (0.29), residues: 301 loop : -3.34 (0.22), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 113 HIS 0.008 0.003 HIS H 107 PHE 0.024 0.003 PHE H 71 TYR 0.021 0.003 TYR b 62 ARG 0.025 0.001 ARG H 102 Details of bonding type rmsd hydrogen bonds : bond 0.14308 ( 211) hydrogen bonds : angle 6.66526 ( 582) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.41650 ( 2) covalent geometry : bond 0.00578 ( 5740) covalent geometry : angle 0.98160 ( 7813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.596 Fit side-chains REVERT: L 72 ILE cc_start: 0.9129 (mt) cc_final: 0.8779 (pt) REVERT: L 102 VAL cc_start: 0.8596 (t) cc_final: 0.8395 (m) REVERT: H 21 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7021 (tm) REVERT: H 74 SER cc_start: 0.8886 (t) cc_final: 0.8254 (p) REVERT: A 53 SER cc_start: 0.8085 (m) cc_final: 0.7660 (t) REVERT: b 2 LYS cc_start: 0.7997 (tttt) cc_final: 0.7516 (mmtt) REVERT: b 24 ARG cc_start: 0.8211 (mtp180) cc_final: 0.6545 (tpt170) REVERT: b 53 SER cc_start: 0.8613 (m) cc_final: 0.8399 (t) REVERT: b 60 LYS cc_start: 0.8426 (pttm) cc_final: 0.8221 (ptpp) REVERT: b 102 ASP cc_start: 0.8366 (p0) cc_final: 0.8134 (p0) REVERT: C 34 SER cc_start: 0.8797 (m) cc_final: 0.8546 (t) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1980 time to fit residues: 39.9529 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 ASN L 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN b 61 ASN b 77 ASN B 61 ASN C 61 ASN C 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106070 restraints weight = 7361.483| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.74 r_work: 0.3153 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5741 Z= 0.145 Angle : 0.607 7.861 7815 Z= 0.320 Chirality : 0.047 0.143 921 Planarity : 0.005 0.048 1021 Dihedral : 5.097 37.929 808 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.60 % Allowed : 9.42 % Favored : 87.99 % 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: -2.66 (0.28), residues: 739 helix: -0.46 (0.53), residues: 94 sheet: -0.95 (0.28), residues: 323 loop : -3.06 (0.25), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 113 HIS 0.007 0.002 HIS H 108 PHE 0.017 0.002 PHE H 71 TYR 0.015 0.002 TYR H 63 ARG 0.006 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 211) hydrogen bonds : angle 5.23580 ( 582) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.63649 ( 2) covalent geometry : bond 0.00332 ( 5740) covalent geometry : angle 0.60719 ( 7813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.658 Fit side-chains REVERT: L 23 LEU cc_start: 0.8488 (mp) cc_final: 0.8217 (mp) REVERT: L 72 ILE cc_start: 0.9189 (mt) cc_final: 0.8837 (pt) REVERT: H 25 CYS cc_start: 0.7976 (p) cc_final: 0.7622 (t) REVERT: H 85 GLN cc_start: 0.7556 (tp40) cc_final: 0.7017 (tp-100) REVERT: b 2 LYS cc_start: 0.8220 (tttt) cc_final: 0.7613 (mmtt) REVERT: b 24 ARG cc_start: 0.8721 (mtp180) cc_final: 0.6346 (tpt170) REVERT: b 60 LYS cc_start: 0.8874 (pttm) cc_final: 0.8446 (ptpp) REVERT: b 123 ASP cc_start: 0.8987 (t70) cc_final: 0.8558 (t0) REVERT: b 127 GLN cc_start: 0.8899 (mp10) cc_final: 0.8678 (mm110) REVERT: B 47 ARG cc_start: 0.8263 (ptp-170) cc_final: 0.7924 (ptp-110) REVERT: C 16 LYS cc_start: 0.9204 (mttt) cc_final: 0.8857 (mttt) REVERT: C 45 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8043 (mm-30) outliers start: 16 outliers final: 9 residues processed: 136 average time/residue: 0.2194 time to fit residues: 36.7227 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 15 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN A 69 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 ASN B 22 ASN C 22 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105442 restraints weight = 7426.948| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.74 r_work: 0.3145 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5741 Z= 0.107 Angle : 0.533 7.012 7815 Z= 0.282 Chirality : 0.045 0.142 921 Planarity : 0.004 0.039 1021 Dihedral : 4.564 30.916 808 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.41 % Allowed : 11.69 % Favored : 84.90 % 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: -1.89 (0.29), residues: 739 helix: 0.30 (0.56), residues: 94 sheet: -0.27 (0.30), residues: 298 loop : -2.68 (0.26), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 113 HIS 0.004 0.002 HIS H 108 PHE 0.013 0.001 PHE H 71 TYR 0.008 0.001 TYR B 62 ARG 0.005 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 211) hydrogen bonds : angle 4.78632 ( 582) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.79654 ( 2) covalent geometry : bond 0.00235 ( 5740) covalent geometry : angle 0.53323 ( 7813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: L 23 LEU cc_start: 0.8370 (mp) cc_final: 0.8063 (mp) REVERT: L 72 ILE cc_start: 0.9139 (mt) cc_final: 0.8845 (pt) REVERT: H 21 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7030 (tm) REVERT: H 25 CYS cc_start: 0.8113 (p) cc_final: 0.7898 (t) REVERT: H 102 ARG cc_start: 0.8650 (ttt90) cc_final: 0.7973 (ttt90) REVERT: b 2 LYS cc_start: 0.8262 (tttt) cc_final: 0.7677 (mmtt) REVERT: b 16 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8626 (mtmp) REVERT: b 24 ARG cc_start: 0.8661 (mtp180) cc_final: 0.6310 (tpt170) REVERT: b 60 LYS cc_start: 0.8834 (pttm) cc_final: 0.8432 (ptpp) REVERT: b 123 ASP cc_start: 0.8967 (t70) cc_final: 0.8617 (t0) REVERT: B 20 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8676 (t) REVERT: B 47 ARG cc_start: 0.8203 (ptp-170) cc_final: 0.7954 (ptp-110) REVERT: C 16 LYS cc_start: 0.9260 (mttt) cc_final: 0.9034 (mttt) REVERT: C 45 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 93 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.9011 (m) outliers start: 21 outliers final: 10 residues processed: 130 average time/residue: 0.2077 time to fit residues: 33.6403 Evaluate side-chains 114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097286 restraints weight = 7547.145| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.68 r_work: 0.3028 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5741 Z= 0.260 Angle : 0.643 5.648 7815 Z= 0.344 Chirality : 0.052 0.157 921 Planarity : 0.005 0.042 1021 Dihedral : 5.107 35.815 808 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.06 % Allowed : 12.82 % Favored : 83.12 % 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: -2.15 (0.29), residues: 739 helix: -0.30 (0.54), residues: 96 sheet: -0.60 (0.29), residues: 329 loop : -2.71 (0.27), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 113 HIS 0.006 0.003 HIS L 100 PHE 0.014 0.002 PHE H 71 TYR 0.021 0.002 TYR L 37 ARG 0.005 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 211) hydrogen bonds : angle 5.13837 ( 582) SS BOND : bond 0.00371 ( 1) SS BOND : angle 1.71408 ( 2) covalent geometry : bond 0.00616 ( 5740) covalent geometry : angle 0.64260 ( 7813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: L 47 HIS cc_start: 0.7721 (p-80) cc_final: 0.7514 (p-80) REVERT: H 71 PHE cc_start: 0.8481 (m-10) cc_final: 0.8234 (m-10) REVERT: A 123 ASP cc_start: 0.8841 (t70) cc_final: 0.8417 (t0) REVERT: b 2 LYS cc_start: 0.8476 (tttt) cc_final: 0.7776 (mmtt) REVERT: b 24 ARG cc_start: 0.9141 (mtp180) cc_final: 0.6787 (tpt170) REVERT: b 60 LYS cc_start: 0.8967 (pttm) cc_final: 0.8615 (ptpp) REVERT: b 123 ASP cc_start: 0.9209 (t70) cc_final: 0.8906 (t0) REVERT: B 47 ARG cc_start: 0.8572 (ptp-170) cc_final: 0.8204 (ptp-110) REVERT: B 61 ASN cc_start: 0.8595 (m-40) cc_final: 0.8307 (m-40) REVERT: C 2 LYS cc_start: 0.8587 (tttt) cc_final: 0.6551 (mmtt) REVERT: C 45 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8093 (mm-30) REVERT: C 87 GLN cc_start: 0.9111 (mt0) cc_final: 0.8827 (mt0) REVERT: C 121 LEU cc_start: 0.8891 (mm) cc_final: 0.8554 (mt) REVERT: C 122 ILE cc_start: 0.8551 (pt) cc_final: 0.8089 (mm) outliers start: 25 outliers final: 18 residues processed: 121 average time/residue: 0.1888 time to fit residues: 29.1628 Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 122 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100584 restraints weight = 7404.759| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.70 r_work: 0.3078 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5741 Z= 0.117 Angle : 0.533 5.888 7815 Z= 0.285 Chirality : 0.046 0.148 921 Planarity : 0.004 0.041 1021 Dihedral : 4.579 29.646 808 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.06 % Allowed : 13.64 % Favored : 82.31 % 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: -1.91 (0.29), residues: 739 helix: 0.17 (0.55), residues: 96 sheet: -0.41 (0.28), residues: 324 loop : -2.69 (0.27), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.010 0.001 PHE H 71 TYR 0.010 0.001 TYR B 62 ARG 0.007 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 211) hydrogen bonds : angle 4.77550 ( 582) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.91436 ( 2) covalent geometry : bond 0.00265 ( 5740) covalent geometry : angle 0.53317 ( 7813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: L 72 ILE cc_start: 0.9177 (mt) cc_final: 0.8836 (pt) REVERT: H 21 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6797 (tm) REVERT: b 2 LYS cc_start: 0.8491 (tttt) cc_final: 0.7825 (mmtt) REVERT: b 4 GLU cc_start: 0.8254 (pt0) cc_final: 0.7874 (mt-10) REVERT: b 24 ARG cc_start: 0.8968 (mtp180) cc_final: 0.6394 (tpt170) REVERT: b 60 LYS cc_start: 0.8949 (pttm) cc_final: 0.8597 (ptpp) REVERT: b 123 ASP cc_start: 0.9167 (t70) cc_final: 0.8742 (t0) REVERT: B 47 ARG cc_start: 0.8547 (ptp-170) cc_final: 0.8256 (ptp-110) REVERT: B 61 ASN cc_start: 0.8668 (m-40) cc_final: 0.8268 (m-40) REVERT: C 2 LYS cc_start: 0.8539 (tttt) cc_final: 0.6544 (mmtt) REVERT: C 45 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7930 (mm-30) REVERT: C 87 GLN cc_start: 0.9208 (mt0) cc_final: 0.8933 (mt0) REVERT: C 93 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9176 (t) REVERT: C 121 LEU cc_start: 0.8780 (mm) cc_final: 0.8462 (mt) REVERT: C 122 ILE cc_start: 0.8633 (pt) cc_final: 0.8115 (mm) outliers start: 25 outliers final: 15 residues processed: 125 average time/residue: 0.2103 time to fit residues: 33.2819 Evaluate side-chains 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN C 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101671 restraints weight = 7373.193| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.66 r_work: 0.3077 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5741 Z= 0.118 Angle : 0.530 7.227 7815 Z= 0.280 Chirality : 0.046 0.146 921 Planarity : 0.004 0.041 1021 Dihedral : 4.365 29.682 808 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.38 % Allowed : 14.45 % Favored : 81.17 % 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: -1.70 (0.29), residues: 739 helix: 0.39 (0.56), residues: 96 sheet: -0.15 (0.30), residues: 306 loop : -2.60 (0.26), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.010 0.001 PHE H 71 TYR 0.010 0.001 TYR B 62 ARG 0.006 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 211) hydrogen bonds : angle 4.60562 ( 582) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.74059 ( 2) covalent geometry : bond 0.00267 ( 5740) covalent geometry : angle 0.52983 ( 7813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: L 72 ILE cc_start: 0.9225 (mt) cc_final: 0.8903 (pt) REVERT: H 21 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6816 (tm) REVERT: H 105 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7236 (t0) REVERT: b 2 LYS cc_start: 0.8477 (tttt) cc_final: 0.7728 (mmtt) REVERT: b 4 GLU cc_start: 0.8266 (pt0) cc_final: 0.7829 (mt-10) REVERT: b 24 ARG cc_start: 0.8970 (mtp180) cc_final: 0.6247 (tpt170) REVERT: b 60 LYS cc_start: 0.8944 (pttm) cc_final: 0.8596 (ptpp) REVERT: b 123 ASP cc_start: 0.9180 (t70) cc_final: 0.8733 (t0) REVERT: B 47 ARG cc_start: 0.8536 (ptp-170) cc_final: 0.8237 (ptp-110) REVERT: B 61 ASN cc_start: 0.8666 (m-40) cc_final: 0.8258 (m-40) REVERT: C 2 LYS cc_start: 0.8529 (tttt) cc_final: 0.6485 (mmtt) REVERT: C 45 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8182 (mm-30) REVERT: C 87 GLN cc_start: 0.9166 (mt0) cc_final: 0.8918 (mt0) REVERT: C 121 LEU cc_start: 0.8738 (mm) cc_final: 0.8427 (mt) REVERT: C 122 ILE cc_start: 0.8604 (pt) cc_final: 0.8032 (mm) outliers start: 27 outliers final: 15 residues processed: 121 average time/residue: 0.1984 time to fit residues: 30.5131 Evaluate side-chains 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 67 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 84 GLN A 127 GLN C 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102700 restraints weight = 7387.102| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.67 r_work: 0.3100 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5741 Z= 0.104 Angle : 0.514 7.027 7815 Z= 0.272 Chirality : 0.046 0.139 921 Planarity : 0.004 0.038 1021 Dihedral : 4.177 27.319 808 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.92 % Allowed : 15.91 % Favored : 81.17 % 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: -1.46 (0.29), residues: 739 helix: 0.57 (0.56), residues: 96 sheet: 0.04 (0.30), residues: 296 loop : -2.41 (0.26), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.011 0.001 PHE H 71 TYR 0.008 0.001 TYR B 62 ARG 0.007 0.000 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 211) hydrogen bonds : angle 4.47780 ( 582) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.63097 ( 2) covalent geometry : bond 0.00232 ( 5740) covalent geometry : angle 0.51436 ( 7813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: L 72 ILE cc_start: 0.9157 (mt) cc_final: 0.8930 (pt) REVERT: H 21 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6914 (tm) REVERT: H 105 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7144 (t0) REVERT: b 2 LYS cc_start: 0.8521 (tttt) cc_final: 0.7835 (mmtt) REVERT: b 4 GLU cc_start: 0.8197 (pt0) cc_final: 0.7777 (mt-10) REVERT: b 16 LYS cc_start: 0.9024 (mttp) cc_final: 0.8618 (mmtp) REVERT: b 24 ARG cc_start: 0.8936 (mtp180) cc_final: 0.6176 (tpt170) REVERT: b 60 LYS cc_start: 0.8937 (pttm) cc_final: 0.8598 (ptpp) REVERT: b 123 ASP cc_start: 0.9174 (t70) cc_final: 0.8749 (t0) REVERT: B 47 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.8212 (ptp-110) REVERT: B 61 ASN cc_start: 0.8641 (m-40) cc_final: 0.8245 (m-40) REVERT: C 2 LYS cc_start: 0.8515 (tttt) cc_final: 0.6513 (mmtt) REVERT: C 87 GLN cc_start: 0.9111 (mt0) cc_final: 0.8854 (mt0) REVERT: C 98 GLN cc_start: 0.8777 (tt0) cc_final: 0.8564 (tt0) REVERT: C 121 LEU cc_start: 0.8719 (mm) cc_final: 0.8413 (mt) REVERT: C 122 ILE cc_start: 0.8557 (pt) cc_final: 0.7985 (mm) outliers start: 18 outliers final: 15 residues processed: 114 average time/residue: 0.1832 time to fit residues: 26.8301 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 59 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 84 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098159 restraints weight = 7379.136| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.63 r_work: 0.3035 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.005 0.036 5741 Z= 0.209 Angle : 0.598 6.666 7815 Z= 0.316 Chirality : 0.050 0.149 921 Planarity : 0.004 0.042 1021 Dihedral : 4.679 32.236 808 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.06 % Allowed : 14.94 % Favored : 81.01 % 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: -1.77 (0.29), residues: 739 helix: 0.06 (0.54), residues: 96 sheet: -0.32 (0.29), residues: 324 loop : -2.51 (0.27), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 113 HIS 0.004 0.002 HIS L 100 PHE 0.031 0.002 PHE H 71 TYR 0.017 0.002 TYR B 62 ARG 0.004 0.001 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 211) hydrogen bonds : angle 4.84488 ( 582) SS BOND : bond 0.00303 ( 1) SS BOND : angle 1.40942 ( 2) covalent geometry : bond 0.00495 ( 5740) covalent geometry : angle 0.59732 ( 7813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.811 Fit side-chains REVERT: L 72 ILE cc_start: 0.9094 (mt) cc_final: 0.8777 (pt) REVERT: L 75 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7868 (mtmm) REVERT: L 109 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8077 (tp) REVERT: H 105 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7306 (t0) REVERT: b 2 LYS cc_start: 0.8565 (tttt) cc_final: 0.7846 (mmtt) REVERT: b 24 ARG cc_start: 0.9090 (mtp180) cc_final: 0.6462 (tpt170) REVERT: b 60 LYS cc_start: 0.8966 (pttm) cc_final: 0.8662 (ptpp) REVERT: b 123 ASP cc_start: 0.9217 (t70) cc_final: 0.8923 (t0) REVERT: B 47 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.8267 (ptp-110) REVERT: B 61 ASN cc_start: 0.8697 (m-40) cc_final: 0.8317 (m-40) REVERT: C 2 LYS cc_start: 0.8561 (tttt) cc_final: 0.6478 (mmtt) REVERT: C 87 GLN cc_start: 0.9213 (mt0) cc_final: 0.8957 (mt0) REVERT: C 121 LEU cc_start: 0.8870 (mm) cc_final: 0.8579 (mt) REVERT: C 122 ILE cc_start: 0.8651 (pt) cc_final: 0.8102 (mm) outliers start: 25 outliers final: 18 residues processed: 120 average time/residue: 0.2179 time to fit residues: 33.2060 Evaluate side-chains 121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 84 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102212 restraints weight = 7375.708| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.65 r_work: 0.3087 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5741 Z= 0.105 Angle : 0.526 7.002 7815 Z= 0.279 Chirality : 0.046 0.150 921 Planarity : 0.004 0.040 1021 Dihedral : 4.245 26.748 808 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.44 % Allowed : 17.05 % Favored : 80.52 % 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: -1.53 (0.29), residues: 739 helix: 0.50 (0.56), residues: 96 sheet: -0.14 (0.29), residues: 322 loop : -2.48 (0.27), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.020 0.001 PHE H 71 TYR 0.011 0.001 TYR H 63 ARG 0.007 0.000 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 211) hydrogen bonds : angle 4.53406 ( 582) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.65461 ( 2) covalent geometry : bond 0.00232 ( 5740) covalent geometry : angle 0.52644 ( 7813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.662 Fit side-chains REVERT: L 72 ILE cc_start: 0.9122 (mt) cc_final: 0.8883 (pt) REVERT: H 21 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6530 (tm) REVERT: H 92 GLU cc_start: 0.7397 (pt0) cc_final: 0.6940 (pm20) REVERT: H 105 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7124 (t0) REVERT: b 2 LYS cc_start: 0.8544 (tttt) cc_final: 0.7839 (mmtt) REVERT: b 4 GLU cc_start: 0.8248 (pt0) cc_final: 0.7852 (mt-10) REVERT: b 24 ARG cc_start: 0.8950 (mtp180) cc_final: 0.6267 (tpt170) REVERT: b 60 LYS cc_start: 0.8962 (pttm) cc_final: 0.8615 (ptpp) REVERT: b 123 ASP cc_start: 0.9184 (t70) cc_final: 0.8751 (t0) REVERT: B 47 ARG cc_start: 0.8483 (ptp-170) cc_final: 0.8190 (ptp-110) REVERT: B 61 ASN cc_start: 0.8654 (m-40) cc_final: 0.8242 (m-40) REVERT: C 2 LYS cc_start: 0.8524 (tttt) cc_final: 0.6481 (mmtt) REVERT: C 87 GLN cc_start: 0.9104 (mt0) cc_final: 0.8844 (mt0) REVERT: C 98 GLN cc_start: 0.8827 (tt0) cc_final: 0.8583 (tt0) REVERT: C 121 LEU cc_start: 0.8706 (mm) cc_final: 0.8401 (mt) REVERT: C 122 ILE cc_start: 0.8632 (pt) cc_final: 0.8043 (mm) outliers start: 15 outliers final: 12 residues processed: 116 average time/residue: 0.2036 time to fit residues: 29.8790 Evaluate side-chains 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 67 optimal weight: 0.0370 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 84 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098976 restraints weight = 7574.803| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.67 r_work: 0.3047 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5741 Z= 0.174 Angle : 0.570 7.426 7815 Z= 0.302 Chirality : 0.048 0.152 921 Planarity : 0.004 0.042 1021 Dihedral : 4.478 30.049 808 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.08 % Allowed : 16.56 % Favored : 80.36 % 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: -1.60 (0.29), residues: 739 helix: 0.26 (0.55), residues: 96 sheet: -0.17 (0.29), residues: 322 loop : -2.46 (0.27), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 113 HIS 0.003 0.002 HIS L 100 PHE 0.008 0.001 PHE H 71 TYR 0.015 0.002 TYR B 62 ARG 0.006 0.001 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 211) hydrogen bonds : angle 4.72085 ( 582) SS BOND : bond 0.00255 ( 1) SS BOND : angle 1.24827 ( 2) covalent geometry : bond 0.00412 ( 5740) covalent geometry : angle 0.56972 ( 7813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.614 Fit side-chains REVERT: L 72 ILE cc_start: 0.9093 (mt) cc_final: 0.8801 (pt) REVERT: H 21 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6347 (tm) REVERT: H 105 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7259 (t0) REVERT: A 127 GLN cc_start: 0.9093 (mp10) cc_final: 0.8796 (mm-40) REVERT: b 2 LYS cc_start: 0.8553 (tttt) cc_final: 0.7846 (mmtt) REVERT: b 24 ARG cc_start: 0.9014 (mtp180) cc_final: 0.6384 (tpt170) REVERT: b 60 LYS cc_start: 0.9000 (pttm) cc_final: 0.8674 (ptpp) REVERT: b 123 ASP cc_start: 0.9213 (t70) cc_final: 0.8911 (t0) REVERT: B 47 ARG cc_start: 0.8555 (ptp-170) cc_final: 0.8231 (ptp-110) REVERT: B 61 ASN cc_start: 0.8649 (m-40) cc_final: 0.8238 (m-40) REVERT: C 2 LYS cc_start: 0.8538 (tttt) cc_final: 0.6522 (mmtt) REVERT: C 87 GLN cc_start: 0.9206 (mt0) cc_final: 0.8900 (mt0) REVERT: C 121 LEU cc_start: 0.8826 (mm) cc_final: 0.8529 (mt) REVERT: C 122 ILE cc_start: 0.8558 (pt) cc_final: 0.8035 (mm) outliers start: 19 outliers final: 15 residues processed: 120 average time/residue: 0.2068 time to fit residues: 31.9816 Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 84 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097113 restraints weight = 7551.249| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.65 r_work: 0.3013 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5741 Z= 0.231 Angle : 0.629 7.525 7815 Z= 0.333 Chirality : 0.051 0.162 921 Planarity : 0.004 0.042 1021 Dihedral : 4.773 31.694 808 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.92 % Allowed : 16.88 % Favored : 80.19 % 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: -1.73 (0.29), residues: 739 helix: -0.05 (0.54), residues: 96 sheet: -0.23 (0.29), residues: 325 loop : -2.52 (0.27), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 50 HIS 0.004 0.002 HIS L 100 PHE 0.010 0.001 PHE H 98 TYR 0.018 0.002 TYR B 62 ARG 0.006 0.001 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 211) hydrogen bonds : angle 4.90961 ( 582) SS BOND : bond 0.00332 ( 1) SS BOND : angle 1.57056 ( 2) covalent geometry : bond 0.00551 ( 5740) covalent geometry : angle 0.62901 ( 7813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3201.03 seconds wall clock time: 56 minutes 10.80 seconds (3370.80 seconds total)