Starting phenix.real_space_refine on Tue Dec 31 20:59:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zxo_15012/12_2024/7zxo_15012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zxo_15012/12_2024/7zxo_15012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zxo_15012/12_2024/7zxo_15012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zxo_15012/12_2024/7zxo_15012.map" model { file = "/net/cci-nas-00/data/ceres_data/7zxo_15012/12_2024/7zxo_15012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zxo_15012/12_2024/7zxo_15012.cif" } resolution = 2.5 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= 0.002 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 156 5.16 5 C 11328 2.51 5 N 2712 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 17016 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 5.82, per 1000 atoms: 0.34 Number of scatterers: 17016 At special positions: 0 Unit cell: (103.986, 93.522, 153.69, 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 156 16.00 O 2820 8.00 N 2712 7.00 C 11328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " 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: 4.36 Conformation dependent library (CDL) restraints added in 2.1 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 74.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 103 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 157 Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 103 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 157 Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 103 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 157 Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG D 22 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 103 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 157 Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 103 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 157 Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG F 22 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 103 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 157 Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 103 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 157 Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 103 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 157 Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 103 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 157 Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG J 22 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 103 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 157 Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG K 22 " --> pdb=" O THR K 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 103 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 157 Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 103 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 157 Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3996 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: 5.05 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5052 1.35 - 1.46: 4516 1.46 - 1.58: 7712 1.58 - 1.70: 0 1.70 - 1.81: 216 Bond restraints: 17496 Sorted by residual: bond pdb=" CB PRO B 87 " pdb=" CG PRO B 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO H 87 " pdb=" CG PRO H 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO E 87 " pdb=" CG PRO E 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO F 87 " pdb=" CG PRO F 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO C 87 " pdb=" CG PRO C 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 ... (remaining 17491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 23320 1.42 - 2.84: 488 2.84 - 4.27: 60 4.27 - 5.69: 24 5.69 - 7.11: 12 Bond angle restraints: 23904 Sorted by residual: angle pdb=" CA PRO D 87 " pdb=" N PRO D 87 " pdb=" CD PRO D 87 " ideal model delta sigma weight residual 112.00 104.89 7.11 1.40e+00 5.10e-01 2.58e+01 angle pdb=" CA PRO K 87 " pdb=" N PRO K 87 " pdb=" CD PRO K 87 " ideal model delta sigma weight residual 112.00 104.90 7.10 1.40e+00 5.10e-01 2.57e+01 angle pdb=" CA PRO E 87 " pdb=" N PRO E 87 " pdb=" CD PRO E 87 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA PRO J 87 " pdb=" N PRO J 87 " pdb=" CD PRO J 87 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA PRO B 87 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 112.00 104.93 7.07 1.40e+00 5.10e-01 2.55e+01 ... (remaining 23899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 8295 11.94 - 23.87: 1047 23.87 - 35.81: 507 35.81 - 47.74: 120 47.74 - 59.68: 120 Dihedral angle restraints: 10089 sinusoidal: 3789 harmonic: 6300 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual 93.00 126.60 -33.60 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" CA SER J 42 " pdb=" C SER J 42 " pdb=" N VAL J 43 " pdb=" CA VAL J 43 " ideal model delta harmonic sigma weight residual -180.00 -163.92 -16.08 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA SER D 42 " pdb=" C SER D 42 " pdb=" N VAL D 43 " pdb=" CA VAL D 43 " ideal model delta harmonic sigma weight residual -180.00 -163.92 -16.08 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 10086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2018 0.035 - 0.070: 607 0.070 - 0.105: 187 0.105 - 0.140: 20 0.140 - 0.175: 24 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA THR E 86 " pdb=" N THR E 86 " pdb=" C THR E 86 " pdb=" CB THR E 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA THR D 86 " pdb=" N THR D 86 " pdb=" C THR D 86 " pdb=" CB THR D 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA THR L 86 " pdb=" N THR L 86 " pdb=" C THR L 86 " pdb=" CB THR L 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 2853 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 86 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO K 87 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO K 87 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO K 87 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 86 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO D 87 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 86 " 0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 87 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 87 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 87 " 0.064 5.00e-02 4.00e+02 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 81 2.60 - 3.18: 14358 3.18 - 3.75: 29570 3.75 - 4.33: 35099 4.33 - 4.90: 59771 Nonbonded interactions: 138879 Sorted by model distance: nonbonded pdb=" SG CYS K 60 " pdb=" SG CYS K 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 60 " pdb=" SG CYS B 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS I 60 " pdb=" SG CYS I 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 60 " pdb=" SG CYS C 173 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F 60 " pdb=" SG CYS F 173 " model vdw 2.030 3.760 ... (remaining 138874 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 4.480 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 33.190 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.003 0.086 17496 Z= 0.204 Angle : 0.523 7.112 23904 Z= 0.305 Chirality : 0.040 0.175 2856 Planarity : 0.008 0.117 2856 Dihedral : 15.391 59.678 5976 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.36 % Allowed : 19.39 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.16), residues: 2076 helix: 4.15 (0.10), residues: 1500 sheet: 1.48 (0.48), residues: 132 loop : -2.28 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.002 0.001 HIS K 94 PHE 0.011 0.001 PHE I 180 TYR 0.008 0.001 TYR J 65 ARG 0.001 0.000 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 298 time to evaluate : 2.028 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 322 average time/residue: 1.1679 time to fit residues: 425.4191 Evaluate side-chains 248 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17496 Z= 0.166 Angle : 0.477 4.926 23904 Z= 0.262 Chirality : 0.040 0.158 2856 Planarity : 0.006 0.078 2856 Dihedral : 3.875 14.833 2292 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.56 % Allowed : 20.60 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.16), residues: 2076 helix: 4.24 (0.09), residues: 1488 sheet: 1.39 (0.46), residues: 132 loop : -2.35 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.002 0.000 HIS H 97 PHE 0.016 0.002 PHE F 180 TYR 0.009 0.001 TYR A 65 ARG 0.001 0.000 ARG J 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 256 time to evaluate : 2.004 Fit side-chains REVERT: A 22 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4713 (tpp-160) REVERT: A 93 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7343 (mpp) REVERT: B 93 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7585 (mpp) REVERT: C 22 ARG cc_start: 0.5189 (OUTLIER) cc_final: 0.4643 (ttt180) REVERT: D 22 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4715 (tpp-160) REVERT: D 93 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7352 (mpp) REVERT: E 93 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7562 (mpp) REVERT: F 22 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.4535 (ttt180) REVERT: G 22 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4711 (tpp-160) REVERT: G 93 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7362 (mpp) REVERT: H 93 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7537 (mpp) REVERT: J 22 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4714 (tpp-160) REVERT: J 93 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7342 (mpp) REVERT: K 93 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7561 (mpp) REVERT: L 22 ARG cc_start: 0.5186 (OUTLIER) cc_final: 0.4527 (ttt180) outliers start: 68 outliers final: 16 residues processed: 296 average time/residue: 1.4551 time to fit residues: 476.1728 Evaluate side-chains 264 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 22 ARG Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 22 ARG Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 200 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 HIS F 97 HIS I 97 HIS J 97 HIS L 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17496 Z= 0.263 Angle : 0.504 5.473 23904 Z= 0.275 Chirality : 0.041 0.175 2856 Planarity : 0.005 0.064 2856 Dihedral : 3.855 15.370 2280 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 4.72 % Allowed : 18.08 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.16), residues: 2076 helix: 4.03 (0.09), residues: 1488 sheet: 1.25 (0.46), residues: 132 loop : -2.14 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 132 HIS 0.005 0.001 HIS H 97 PHE 0.015 0.002 PHE K 180 TYR 0.015 0.002 TYR E 65 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 220 time to evaluate : 2.197 Fit side-chains REVERT: A 93 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7438 (mpp) REVERT: B 22 ARG cc_start: 0.6106 (OUTLIER) cc_final: 0.4526 (tpp-160) REVERT: D 93 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7436 (mpp) REVERT: E 22 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.4528 (tpp-160) REVERT: G 93 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7440 (mpp) REVERT: H 22 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.4526 (tpp-160) REVERT: I 22 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.4406 (tpp-160) REVERT: J 93 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7421 (mpp) REVERT: K 22 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.4516 (tpp-160) outliers start: 90 outliers final: 24 residues processed: 285 average time/residue: 1.3131 time to fit residues: 424.2174 Evaluate side-chains 248 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 0.0470 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17496 Z= 0.144 Angle : 0.440 5.011 23904 Z= 0.239 Chirality : 0.038 0.160 2856 Planarity : 0.004 0.051 2856 Dihedral : 3.700 14.811 2280 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.31 % Allowed : 21.65 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.31 (0.16), residues: 2076 helix: 4.31 (0.09), residues: 1488 sheet: 1.37 (0.46), residues: 132 loop : -2.25 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.003 0.001 HIS E 97 PHE 0.008 0.001 PHE F 180 TYR 0.007 0.001 TYR A 65 ARG 0.003 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 2.055 Fit side-chains REVERT: A 93 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7463 (mpp) REVERT: B 22 ARG cc_start: 0.5333 (OUTLIER) cc_final: 0.4232 (tpp-160) REVERT: C 97 HIS cc_start: 0.7520 (t-90) cc_final: 0.7278 (t-170) REVERT: D 93 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7436 (mpp) REVERT: E 22 ARG cc_start: 0.5325 (OUTLIER) cc_final: 0.4228 (tpp-160) REVERT: F 97 HIS cc_start: 0.7525 (t-90) cc_final: 0.7280 (t-170) REVERT: G 93 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7459 (mpp) REVERT: H 22 ARG cc_start: 0.5329 (OUTLIER) cc_final: 0.4228 (tpp-160) REVERT: I 97 HIS cc_start: 0.7516 (t-90) cc_final: 0.7274 (t-170) REVERT: J 93 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7468 (mpp) REVERT: K 22 ARG cc_start: 0.5337 (OUTLIER) cc_final: 0.4231 (tpp-160) REVERT: L 97 HIS cc_start: 0.7530 (t-90) cc_final: 0.7289 (t-170) outliers start: 44 outliers final: 19 residues processed: 259 average time/residue: 1.3070 time to fit residues: 378.1416 Evaluate side-chains 246 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17496 Z= 0.200 Angle : 0.461 4.970 23904 Z= 0.250 Chirality : 0.039 0.161 2856 Planarity : 0.004 0.046 2856 Dihedral : 3.659 14.315 2280 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 4.45 % Allowed : 19.92 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.16), residues: 2076 helix: 4.25 (0.09), residues: 1488 sheet: 1.31 (0.45), residues: 132 loop : -2.17 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 132 HIS 0.004 0.001 HIS E 97 PHE 0.012 0.002 PHE B 180 TYR 0.013 0.001 TYR E 65 ARG 0.003 0.000 ARG J 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 2.176 Fit side-chains REVERT: A 93 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7498 (mpp) REVERT: B 22 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4366 (tpp-160) REVERT: C 97 HIS cc_start: 0.7558 (t-90) cc_final: 0.7225 (t-170) REVERT: D 93 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7470 (mpp) REVERT: E 22 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.4356 (tpp-160) REVERT: F 97 HIS cc_start: 0.7570 (t-90) cc_final: 0.7251 (t-170) REVERT: G 93 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7495 (mpp) REVERT: H 22 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.4352 (tpp-160) REVERT: I 22 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.4548 (tpp-160) REVERT: I 97 HIS cc_start: 0.7571 (t-90) cc_final: 0.7254 (t-170) REVERT: J 93 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7476 (mpp) REVERT: J 97 HIS cc_start: 0.7708 (t-170) cc_final: 0.7458 (t-170) REVERT: K 22 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.4356 (tpp-160) REVERT: L 97 HIS cc_start: 0.7576 (t-90) cc_final: 0.7258 (t-170) outliers start: 85 outliers final: 21 residues processed: 286 average time/residue: 1.1762 time to fit residues: 380.7588 Evaluate side-chains 240 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17496 Z= 0.175 Angle : 0.456 4.856 23904 Z= 0.248 Chirality : 0.039 0.151 2856 Planarity : 0.004 0.042 2856 Dihedral : 3.605 14.489 2280 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.99 % Allowed : 21.91 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.16), residues: 2076 helix: 4.27 (0.09), residues: 1488 sheet: 1.60 (0.47), residues: 132 loop : -2.15 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 132 HIS 0.004 0.001 HIS E 97 PHE 0.013 0.001 PHE G 180 TYR 0.010 0.001 TYR J 65 ARG 0.001 0.000 ARG L 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 2.082 Fit side-chains REVERT: A 93 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7484 (mpp) REVERT: B 22 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.4371 (tpp-160) REVERT: C 97 HIS cc_start: 0.7599 (t-90) cc_final: 0.7269 (t-170) REVERT: C 156 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8864 (mp) REVERT: E 22 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.4358 (tpp-160) REVERT: F 97 HIS cc_start: 0.7604 (t-90) cc_final: 0.7268 (t-170) REVERT: F 156 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8882 (mp) REVERT: G 93 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7477 (mpp) REVERT: H 22 ARG cc_start: 0.5460 (OUTLIER) cc_final: 0.4357 (tpp-160) REVERT: I 22 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.4567 (tpp-160) REVERT: I 97 HIS cc_start: 0.7606 (t-90) cc_final: 0.7273 (t-170) REVERT: I 156 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8881 (mp) REVERT: J 93 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7486 (mpp) REVERT: J 97 HIS cc_start: 0.7738 (t-170) cc_final: 0.7473 (t-170) REVERT: K 22 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.4353 (tpp-160) REVERT: L 97 HIS cc_start: 0.7604 (t-90) cc_final: 0.7271 (t-170) REVERT: L 156 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8872 (mp) outliers start: 57 outliers final: 18 residues processed: 263 average time/residue: 1.3323 time to fit residues: 391.4438 Evaluate side-chains 248 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 17496 Z= 0.357 Angle : 0.546 5.056 23904 Z= 0.297 Chirality : 0.043 0.162 2856 Planarity : 0.004 0.043 2856 Dihedral : 3.830 15.767 2280 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.41 % Allowed : 22.27 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.16), residues: 2076 helix: 3.87 (0.10), residues: 1488 sheet: 1.39 (0.46), residues: 132 loop : -1.96 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 133 HIS 0.004 0.001 HIS E 97 PHE 0.017 0.003 PHE J 180 TYR 0.018 0.002 TYR D 65 ARG 0.002 0.001 ARG J 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 1.863 Fit side-chains REVERT: A 93 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7487 (mpp) REVERT: B 22 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.4512 (tpp-160) REVERT: B 156 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8930 (mp) REVERT: C 97 HIS cc_start: 0.7666 (t-90) cc_final: 0.7291 (t-170) REVERT: E 22 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.4502 (tpp-160) REVERT: F 97 HIS cc_start: 0.7672 (t-90) cc_final: 0.7296 (t-170) REVERT: G 93 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7484 (mpp) REVERT: H 22 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.4504 (tpp-160) REVERT: H 156 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8936 (mp) REVERT: I 97 HIS cc_start: 0.7676 (t-90) cc_final: 0.7302 (t-170) REVERT: J 93 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7493 (mpp) REVERT: K 22 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.4545 (tpp-160) REVERT: L 97 HIS cc_start: 0.7679 (t-90) cc_final: 0.7304 (t-170) outliers start: 46 outliers final: 21 residues processed: 248 average time/residue: 1.4183 time to fit residues: 389.9351 Evaluate side-chains 245 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17496 Z= 0.171 Angle : 0.472 4.796 23904 Z= 0.256 Chirality : 0.039 0.150 2856 Planarity : 0.003 0.040 2856 Dihedral : 3.671 14.912 2280 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.25 % Allowed : 23.85 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.17), residues: 2076 helix: 4.16 (0.10), residues: 1488 sheet: 1.70 (0.47), residues: 132 loop : -2.08 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 132 HIS 0.004 0.001 HIS K 97 PHE 0.011 0.001 PHE D 180 TYR 0.009 0.001 TYR A 65 ARG 0.001 0.000 ARG G 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 1.947 Fit side-chains REVERT: B 22 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.4459 (tpp-160) REVERT: C 97 HIS cc_start: 0.7623 (t-90) cc_final: 0.7302 (t-170) REVERT: C 156 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8882 (mp) REVERT: E 22 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.4456 (tpp-160) REVERT: E 156 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8877 (mp) REVERT: F 97 HIS cc_start: 0.7637 (t-90) cc_final: 0.7315 (t-170) REVERT: F 156 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8895 (mp) REVERT: H 22 ARG cc_start: 0.5633 (OUTLIER) cc_final: 0.4461 (tpp-160) REVERT: I 97 HIS cc_start: 0.7618 (t-90) cc_final: 0.7306 (t-170) REVERT: I 156 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8897 (mp) REVERT: K 22 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4447 (tpp-160) REVERT: K 156 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8867 (mp) REVERT: L 97 HIS cc_start: 0.7642 (t-90) cc_final: 0.7328 (t-170) REVERT: L 156 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8896 (mp) outliers start: 43 outliers final: 22 residues processed: 267 average time/residue: 1.3946 time to fit residues: 413.1282 Evaluate side-chains 254 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 156 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 143 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN C 97 HIS D 98 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN I 97 HIS J 97 HIS ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17496 Z= 0.157 Angle : 0.470 4.989 23904 Z= 0.254 Chirality : 0.038 0.152 2856 Planarity : 0.003 0.040 2856 Dihedral : 3.527 14.900 2280 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.57 % Allowed : 24.48 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.17), residues: 2076 helix: 4.25 (0.10), residues: 1488 sheet: 1.92 (0.49), residues: 132 loop : -2.18 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 132 HIS 0.004 0.001 HIS D 97 PHE 0.010 0.001 PHE F 180 TYR 0.008 0.001 TYR E 65 ARG 0.002 0.000 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 2.025 Fit side-chains REVERT: B 22 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.4391 (tpp-160) REVERT: C 97 HIS cc_start: 0.7497 (t70) cc_final: 0.7283 (t-170) REVERT: E 22 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4365 (tpp-160) REVERT: F 97 HIS cc_start: 0.7583 (t-90) cc_final: 0.7284 (t-170) REVERT: H 22 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.4382 (tpp-160) REVERT: I 97 HIS cc_start: 0.7531 (t70) cc_final: 0.7311 (t-170) REVERT: K 22 ARG cc_start: 0.5571 (OUTLIER) cc_final: 0.4379 (tpp-160) REVERT: L 97 HIS cc_start: 0.7604 (t-90) cc_final: 0.7308 (t-170) outliers start: 30 outliers final: 14 residues processed: 262 average time/residue: 1.4248 time to fit residues: 412.8870 Evaluate side-chains 246 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17496 Z= 0.276 Angle : 0.522 5.336 23904 Z= 0.284 Chirality : 0.041 0.157 2856 Planarity : 0.004 0.041 2856 Dihedral : 3.703 14.908 2280 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.52 % Allowed : 24.74 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.16), residues: 2076 helix: 3.94 (0.10), residues: 1488 sheet: 1.53 (0.46), residues: 132 loop : -2.01 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 133 HIS 0.005 0.001 HIS E 97 PHE 0.014 0.002 PHE K 180 TYR 0.015 0.002 TYR J 65 ARG 0.003 0.000 ARG F 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 2.037 Fit side-chains REVERT: A 156 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8881 (mp) REVERT: B 22 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.4397 (tpp-160) REVERT: C 97 HIS cc_start: 0.7627 (t70) cc_final: 0.7405 (t-170) REVERT: D 156 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8884 (mp) REVERT: E 22 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.4509 (tpp-160) REVERT: F 97 HIS cc_start: 0.7645 (t-90) cc_final: 0.7325 (t-170) REVERT: G 156 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8889 (mp) REVERT: H 22 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.4380 (tpp-160) REVERT: H 156 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8923 (mp) REVERT: I 97 HIS cc_start: 0.7630 (t70) cc_final: 0.7414 (t-170) REVERT: J 156 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8884 (mp) REVERT: K 22 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.4508 (tpp-160) REVERT: L 97 HIS cc_start: 0.7659 (t-90) cc_final: 0.7338 (t-170) outliers start: 29 outliers final: 12 residues processed: 249 average time/residue: 1.4964 time to fit residues: 411.0126 Evaluate side-chains 244 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 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 = 0.3530 r_free = 0.3530 target = 0.107305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.072506 restraints weight = 24954.358| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.99 r_work: 0.2745 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17496 Z= 0.183 Angle : 0.489 5.395 23904 Z= 0.265 Chirality : 0.039 0.152 2856 Planarity : 0.003 0.040 2856 Dihedral : 3.615 14.898 2280 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.89 % Allowed : 25.37 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.16), residues: 2076 helix: 4.09 (0.10), residues: 1488 sheet: 1.68 (0.47), residues: 132 loop : -2.11 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 132 HIS 0.005 0.001 HIS H 97 PHE 0.012 0.002 PHE J 180 TYR 0.010 0.001 TYR J 65 ARG 0.003 0.000 ARG F 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6268.02 seconds wall clock time: 114 minutes 0.66 seconds (6840.66 seconds total)