Starting phenix.real_space_refine on Tue Feb 13 15:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl4_14777/02_2024/7zl4_14777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl4_14777/02_2024/7zl4_14777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl4_14777/02_2024/7zl4_14777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl4_14777/02_2024/7zl4_14777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl4_14777/02_2024/7zl4_14777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zl4_14777/02_2024/7zl4_14777.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 2088 2.51 5 N 582 2.21 5 O 708 1.98 5 H 3291 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6678 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2017 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2226 Classifications: {'peptide': 155} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "C" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2226 Classifications: {'peptide': 155} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 209 Classifications: {'peptide': 14} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 13} Time building chain proxies: 4.15, per 1000 atoms: 0.62 Number of scatterers: 6678 At special positions: 0 Unit cell: (59.5654, 68.6297, 103.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 708 8.00 N 582 7.00 C 2088 6.00 H 3291 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 63 " distance=2.04 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 63 " distance=2.04 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 63 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.68 Conformation dependent library (CDL) restraints added in 789.4 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 61.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 4.359A pdb=" N ILE A 59 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 9.023A pdb=" N THR B 3 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS A 29 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 5 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B 11 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 37 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 148 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N THR A 84 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 52 removed outlier: 9.023A pdb=" N THR B 3 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS A 29 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 5 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B 11 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 37 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 removed outlier: 4.359A pdb=" N ILE B 59 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 24 removed outlier: 9.013A pdb=" N THR C 3 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 29 " --> pdb=" O THR C 3 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN C 5 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 11 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS B 37 " --> pdb=" O ASN C 11 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 148 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR B 84 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 52 removed outlier: 9.013A pdb=" N THR C 3 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 29 " --> pdb=" O THR C 3 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN C 5 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 11 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS B 37 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 removed outlier: 4.359A pdb=" N ILE C 59 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 24 removed outlier: 9.000A pdb=" N THR D 3 " --> pdb=" O MET C 27 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C 29 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN D 5 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 11 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 37 " --> pdb=" O ASN D 11 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 148 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR C 84 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 50 through 52 removed outlier: 9.000A pdb=" N THR D 3 " --> pdb=" O MET C 27 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C 29 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN D 5 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 11 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 37 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 99 195 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 3291 1.02 - 1.22: 26 1.22 - 1.42: 1377 1.42 - 1.63: 2019 1.63 - 1.83: 12 Bond restraints: 6725 Sorted by residual: bond pdb=" ND2 ASN C 135 " pdb="HD22 ASN C 135 " ideal model delta sigma weight residual 0.860 0.992 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" ND2 ASN B 135 " pdb="HD22 ASN B 135 " ideal model delta sigma weight residual 0.860 0.992 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" ND2 ASN A 135 " pdb="HD22 ASN A 135 " ideal model delta sigma weight residual 0.860 0.992 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" ND2 ASN A 87 " pdb="HD22 ASN A 87 " ideal model delta sigma weight residual 0.860 0.982 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" ND2 ASN B 43 " pdb="HD21 ASN B 43 " ideal model delta sigma weight residual 0.860 0.982 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 6720 not shown) Histogram of bond angle deviations from ideal: 100.90 - 107.50: 595 107.50 - 114.09: 7720 114.09 - 120.69: 2088 120.69 - 127.28: 1653 127.28 - 133.87: 42 Bond angle restraints: 12098 Sorted by residual: angle pdb=" N THR B 81 " pdb=" CA THR B 81 " pdb=" C THR B 81 " ideal model delta sigma weight residual 113.38 117.89 -4.51 1.17e+00 7.31e-01 1.48e+01 angle pdb=" N THR C 81 " pdb=" CA THR C 81 " pdb=" C THR C 81 " ideal model delta sigma weight residual 113.38 117.88 -4.50 1.17e+00 7.31e-01 1.48e+01 angle pdb=" N THR A 81 " pdb=" CA THR A 81 " pdb=" C THR A 81 " ideal model delta sigma weight residual 113.38 117.81 -4.43 1.17e+00 7.31e-01 1.44e+01 angle pdb=" N ALA A 102 " pdb=" CA ALA A 102 " pdb=" C ALA A 102 " ideal model delta sigma weight residual 112.38 116.88 -4.50 1.22e+00 6.72e-01 1.36e+01 angle pdb=" N ALA B 102 " pdb=" CA ALA B 102 " pdb=" C ALA B 102 " ideal model delta sigma weight residual 112.38 116.86 -4.48 1.22e+00 6.72e-01 1.35e+01 ... (remaining 12093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2643 17.96 - 35.92: 332 35.92 - 53.89: 153 53.89 - 71.85: 54 71.85 - 89.81: 24 Dihedral angle restraints: 3206 sinusoidal: 1749 harmonic: 1457 Sorted by residual: dihedral pdb=" SG CYS A 16 " pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" CA CYS A 63 " ideal model delta sinusoidal sigma weight residual 79.00 16.81 62.19 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" SG CYS B 16 " pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" CA CYS B 63 " ideal model delta sinusoidal sigma weight residual 79.00 16.82 62.18 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" SG CYS C 16 " pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" CA CYS C 63 " ideal model delta sinusoidal sigma weight residual 79.00 16.84 62.16 1 2.00e+01 2.50e-03 1.28e+01 ... (remaining 3203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 342 0.060 - 0.119: 125 0.119 - 0.179: 59 0.179 - 0.238: 35 0.238 - 0.298: 12 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA ILE A 59 " pdb=" N ILE A 59 " pdb=" C ILE A 59 " pdb=" CB ILE A 59 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 570 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 96 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C TYR B 96 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR B 96 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 97 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 96 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C TYR A 96 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR A 96 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 97 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 96 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C TYR C 96 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR C 96 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN C 97 " 0.014 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 1313 2.30 - 2.88: 14984 2.88 - 3.45: 17694 3.45 - 4.03: 24435 4.03 - 4.60: 35931 Nonbonded interactions: 94357 Sorted by model distance: nonbonded pdb=" H SER A 52 " pdb=" O GLY A 57 " model vdw 1.727 1.850 nonbonded pdb=" H SER B 52 " pdb=" O GLY B 57 " model vdw 1.727 1.850 nonbonded pdb=" H SER C 52 " pdb=" O GLY C 57 " model vdw 1.727 1.850 nonbonded pdb=" HG2 LYS B 86 " pdb=" HZ1 LYS B 86 " model vdw 1.745 2.270 nonbonded pdb=" HG2 LYS C 86 " pdb=" HZ1 LYS C 86 " model vdw 1.745 2.270 ... (remaining 94352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 15 through 155) selection = (chain 'C' and resid 15 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 27.630 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3434 Z= 0.461 Angle : 1.391 6.722 4695 Z= 0.906 Chirality : 0.090 0.298 573 Planarity : 0.005 0.025 623 Dihedral : 16.420 84.834 1178 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.30), residues: 457 helix: None (None), residues: 0 sheet: -1.90 (0.37), residues: 158 loop : -3.36 (0.24), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 42 PHE 0.015 0.003 PHE B 116 TYR 0.010 0.002 TYR B 108 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6380 (tpt) cc_final: 0.5619 (mtt) REVERT: A 100 ARG cc_start: 0.6918 (ttt180) cc_final: 0.6533 (ttt180) REVERT: A 129 PHE cc_start: 0.7924 (m-80) cc_final: 0.7647 (m-80) REVERT: B 5 GLN cc_start: 0.7947 (mt0) cc_final: 0.7535 (mt0) REVERT: B 150 LEU cc_start: 0.8963 (mt) cc_final: 0.8725 (tp) REVERT: C 9 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7864 (mtpp) REVERT: C 24 GLU cc_start: 0.7548 (tt0) cc_final: 0.7203 (tt0) REVERT: C 70 ASP cc_start: 0.7918 (t70) cc_final: 0.7384 (p0) REVERT: C 86 LYS cc_start: 0.8265 (tttm) cc_final: 0.8062 (ttmm) REVERT: C 112 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7330 (mm-40) REVERT: C 150 LEU cc_start: 0.8807 (mt) cc_final: 0.8600 (mt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3330 time to fit residues: 56.2947 Evaluate side-chains 94 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3434 Z= 0.202 Angle : 0.559 6.837 4695 Z= 0.304 Chirality : 0.050 0.147 573 Planarity : 0.004 0.031 623 Dihedral : 4.183 14.896 488 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.64 % Allowed : 17.21 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.33), residues: 457 helix: None (None), residues: 0 sheet: -1.70 (0.41), residues: 151 loop : -2.53 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 PHE 0.017 0.002 PHE C 116 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6416 (tpt) cc_final: 0.5466 (mtt) REVERT: A 42 TRP cc_start: 0.7717 (p90) cc_final: 0.7037 (p90) REVERT: A 73 VAL cc_start: 0.8917 (t) cc_final: 0.8373 (t) REVERT: A 86 LYS cc_start: 0.8973 (tttm) cc_final: 0.8658 (mtpp) REVERT: A 90 SER cc_start: 0.8315 (p) cc_final: 0.8019 (p) REVERT: A 112 GLN cc_start: 0.8895 (mm110) cc_final: 0.8385 (mm110) REVERT: B 5 GLN cc_start: 0.7638 (mt0) cc_final: 0.7339 (mt0) REVERT: B 9 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7620 (mtpp) REVERT: C 70 ASP cc_start: 0.7994 (t70) cc_final: 0.7520 (p0) REVERT: C 92 ASP cc_start: 0.6783 (m-30) cc_final: 0.6457 (m-30) REVERT: C 112 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7243 (mm-40) outliers start: 6 outliers final: 6 residues processed: 104 average time/residue: 0.2867 time to fit residues: 37.1094 Evaluate side-chains 93 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.2980 chunk 34 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3434 Z= 0.183 Angle : 0.510 6.134 4695 Z= 0.276 Chirality : 0.048 0.136 573 Planarity : 0.004 0.062 623 Dihedral : 3.943 13.560 488 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.91 % Allowed : 16.39 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.32 (0.43), residues: 146 loop : -2.25 (0.28), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 PHE 0.011 0.001 PHE C 116 TYR 0.009 0.001 TYR A 108 ARG 0.002 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6502 (tpt) cc_final: 0.5513 (mtt) REVERT: A 42 TRP cc_start: 0.7740 (p90) cc_final: 0.7049 (p90) REVERT: A 86 LYS cc_start: 0.9056 (tttm) cc_final: 0.8709 (mtpp) REVERT: A 90 SER cc_start: 0.8461 (p) cc_final: 0.8225 (p) REVERT: A 112 GLN cc_start: 0.8886 (mm110) cc_final: 0.8285 (tp40) REVERT: B 5 GLN cc_start: 0.7625 (mt0) cc_final: 0.7342 (mt0) REVERT: B 9 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7672 (mtpp) REVERT: C 112 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7404 (mm-40) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.2660 time to fit residues: 31.2477 Evaluate side-chains 87 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3434 Z= 0.211 Angle : 0.496 6.375 4695 Z= 0.263 Chirality : 0.047 0.136 573 Planarity : 0.003 0.050 623 Dihedral : 3.887 12.956 488 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.19 % Allowed : 17.49 % Favored : 80.33 % 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: -2.55 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.06 (0.48), residues: 136 loop : -2.12 (0.27), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 42 PHE 0.011 0.001 PHE B 116 TYR 0.009 0.002 TYR A 108 ARG 0.003 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6731 (tpt) cc_final: 0.5851 (mtt) REVERT: A 42 TRP cc_start: 0.7911 (p90) cc_final: 0.7214 (p90) REVERT: A 112 GLN cc_start: 0.8901 (mm110) cc_final: 0.8399 (mm110) REVERT: B 9 LYS cc_start: 0.8349 (mtmm) cc_final: 0.8043 (mtpp) REVERT: C 27 MET cc_start: 0.7361 (tpt) cc_final: 0.6814 (tpt) REVERT: C 112 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7466 (mm-40) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.2812 time to fit residues: 32.7043 Evaluate side-chains 86 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 43 ASN B 44 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3434 Z= 0.278 Angle : 0.506 6.400 4695 Z= 0.273 Chirality : 0.048 0.147 573 Planarity : 0.004 0.055 623 Dihedral : 4.068 14.297 488 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.55 % Allowed : 16.39 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.34 (0.43), residues: 149 loop : -2.05 (0.27), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 42 PHE 0.010 0.001 PHE B 116 TYR 0.008 0.001 TYR C 108 ARG 0.003 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7066 (tpt) cc_final: 0.6213 (mtt) REVERT: A 112 GLN cc_start: 0.8894 (mm110) cc_final: 0.8421 (mm110) REVERT: C 27 MET cc_start: 0.7301 (tpt) cc_final: 0.6682 (tpt) REVERT: C 33 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 62 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7199 (p) REVERT: C 107 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7764 (tt) REVERT: C 112 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7570 (tp40) outliers start: 13 outliers final: 9 residues processed: 90 average time/residue: 0.2700 time to fit residues: 30.8381 Evaluate side-chains 94 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 8 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3434 Z= 0.243 Angle : 0.498 6.335 4695 Z= 0.269 Chirality : 0.047 0.135 573 Planarity : 0.004 0.052 623 Dihedral : 4.059 15.181 488 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.83 % Allowed : 17.49 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.53 (0.42), residues: 159 loop : -1.93 (0.28), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 42 PHE 0.009 0.001 PHE B 116 TYR 0.008 0.001 TYR A 108 ARG 0.003 0.001 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7287 (tpt) cc_final: 0.6094 (mtt) REVERT: A 112 GLN cc_start: 0.8932 (mm110) cc_final: 0.8410 (mm110) REVERT: B 49 GLU cc_start: 0.8193 (tt0) cc_final: 0.7918 (mt-10) REVERT: C 27 MET cc_start: 0.7141 (tpt) cc_final: 0.6396 (tpt) REVERT: C 33 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 62 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7227 (p) REVERT: C 107 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7740 (tt) REVERT: C 112 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7451 (mm-40) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.2613 time to fit residues: 29.4392 Evaluate side-chains 95 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3434 Z= 0.185 Angle : 0.482 5.915 4695 Z= 0.259 Chirality : 0.047 0.135 573 Planarity : 0.004 0.051 623 Dihedral : 3.931 13.110 488 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.28 % Allowed : 18.31 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.52 (0.41), residues: 159 loop : -1.76 (0.29), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 42 PHE 0.009 0.001 PHE B 116 TYR 0.006 0.001 TYR A 145 ARG 0.002 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7467 (tpt) cc_final: 0.6305 (mtt) REVERT: A 86 LYS cc_start: 0.8818 (tttp) cc_final: 0.8506 (tptp) REVERT: A 112 GLN cc_start: 0.8925 (mm110) cc_final: 0.8678 (mm-40) REVERT: B 49 GLU cc_start: 0.8165 (tt0) cc_final: 0.7905 (mt-10) REVERT: C 62 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7312 (p) REVERT: C 107 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7722 (tt) REVERT: C 112 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7399 (mm-40) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.2645 time to fit residues: 29.8939 Evaluate side-chains 91 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3434 Z= 0.157 Angle : 0.470 5.604 4695 Z= 0.251 Chirality : 0.047 0.132 573 Planarity : 0.003 0.047 623 Dihedral : 3.781 12.817 488 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.73 % Allowed : 18.58 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.34), residues: 457 helix: None (None), residues: 0 sheet: -1.45 (0.41), residues: 159 loop : -1.70 (0.29), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 42 PHE 0.009 0.001 PHE C 116 TYR 0.006 0.001 TYR B 96 ARG 0.002 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7560 (tpt) cc_final: 0.6327 (mtt) REVERT: A 112 GLN cc_start: 0.9065 (mm110) cc_final: 0.8697 (mm-40) REVERT: B 49 GLU cc_start: 0.8140 (tt0) cc_final: 0.7904 (mt-10) REVERT: C 27 MET cc_start: 0.7120 (tpt) cc_final: 0.6473 (tpt) REVERT: C 62 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7321 (p) REVERT: C 107 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7713 (tt) REVERT: C 112 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7357 (mm-40) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.2600 time to fit residues: 30.2668 Evaluate side-chains 89 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3434 Z= 0.147 Angle : 0.469 5.578 4695 Z= 0.249 Chirality : 0.046 0.132 573 Planarity : 0.003 0.047 623 Dihedral : 3.694 12.107 488 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.46 % Allowed : 18.85 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.43 (0.42), residues: 150 loop : -1.54 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 42 PHE 0.009 0.001 PHE C 116 TYR 0.006 0.001 TYR B 96 ARG 0.002 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7654 (tpt) cc_final: 0.6426 (mtt) REVERT: A 86 LYS cc_start: 0.8831 (tttp) cc_final: 0.8525 (tptp) REVERT: A 112 GLN cc_start: 0.9072 (mm110) cc_final: 0.8598 (mm110) REVERT: B 49 GLU cc_start: 0.8125 (tt0) cc_final: 0.7892 (mt-10) REVERT: B 150 LEU cc_start: 0.8872 (mt) cc_final: 0.8576 (mm) REVERT: C 27 MET cc_start: 0.7093 (tpt) cc_final: 0.6474 (tpt) REVERT: C 62 THR cc_start: 0.7472 (OUTLIER) cc_final: 0.7230 (p) REVERT: C 107 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7803 (tt) REVERT: C 112 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7348 (mm-40) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.2912 time to fit residues: 31.8874 Evaluate side-chains 89 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 9 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3434 Z= 0.243 Angle : 0.497 6.001 4695 Z= 0.267 Chirality : 0.047 0.139 573 Planarity : 0.003 0.045 623 Dihedral : 3.899 12.488 488 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.28 % Allowed : 17.76 % Favored : 78.96 % 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: -2.26 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.45 (0.42), residues: 150 loop : -1.58 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 42 PHE 0.008 0.001 PHE B 116 TYR 0.009 0.001 TYR C 108 ARG 0.002 0.001 ARG B 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7637 (tpt) cc_final: 0.6423 (mtt) REVERT: A 60 SER cc_start: 0.8589 (m) cc_final: 0.8343 (p) REVERT: A 112 GLN cc_start: 0.9084 (mm110) cc_final: 0.8602 (mm110) REVERT: B 49 GLU cc_start: 0.8150 (tt0) cc_final: 0.7923 (mt-10) REVERT: B 60 SER cc_start: 0.8254 (m) cc_final: 0.8029 (p) REVERT: B 150 LEU cc_start: 0.8878 (mt) cc_final: 0.8555 (mm) REVERT: C 27 MET cc_start: 0.7026 (tpt) cc_final: 0.6315 (tpt) REVERT: C 62 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7260 (p) REVERT: C 107 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7713 (tt) REVERT: C 112 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7395 (mm-40) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.2599 time to fit residues: 27.9007 Evaluate side-chains 88 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 9 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.122321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.092934 restraints weight = 14464.234| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.43 r_work: 0.3210 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3434 Z= 0.186 Angle : 0.482 5.873 4695 Z= 0.257 Chirality : 0.047 0.132 573 Planarity : 0.003 0.047 623 Dihedral : 3.816 12.360 488 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.01 % Allowed : 18.03 % Favored : 78.96 % 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: -2.22 (0.35), residues: 457 helix: None (None), residues: 0 sheet: -1.41 (0.42), residues: 150 loop : -1.55 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 42 PHE 0.008 0.001 PHE B 116 TYR 0.006 0.001 TYR C 108 ARG 0.002 0.000 ARG B 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.25 seconds wall clock time: 50 minutes 42.42 seconds (3042.42 seconds total)