Starting phenix.real_space_refine on Mon Mar 11 10:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/03_2024/6b3o_7040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/03_2024/6b3o_7040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/03_2024/6b3o_7040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/03_2024/6b3o_7040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/03_2024/6b3o_7040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/03_2024/6b3o_7040.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 36 5.16 5 C 5040 2.51 5 N 1335 2.21 5 O 1569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7980 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2660 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Chain: "B" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2660 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Chain: "C" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2660 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Time building chain proxies: 4.68, per 1000 atoms: 0.59 Number of scatterers: 7980 At special positions: 0 Unit cell: (70.72, 74.8, 202.64, 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 36 16.00 O 1569 8.00 N 1335 7.00 C 5040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS A 780 " - pdb=" SG CYS A 786 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1093 " distance=2.02 Simple disulfide: pdb=" SG CYS A1132 " - pdb=" SG CYS A1177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 775 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 780 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1093 " distance=2.02 Simple disulfide: pdb=" SG CYS B1132 " - pdb=" SG CYS B1177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 780 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1093 " distance=2.02 Simple disulfide: pdb=" SG CYS C1132 " - pdb=" SG CYS C1177 " distance=2.03 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 48.0% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 783 through 791 Processing helix chain 'A' and resid 795 through 807 removed outlier: 4.265A pdb=" N ASN A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 1081 Processing helix chain 'A' and resid 1198 through 1204 Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1231 through 1245 Processing helix chain 'B' and resid 774 through 780 Processing helix chain 'B' and resid 783 through 791 Processing helix chain 'B' and resid 795 through 807 removed outlier: 4.265A pdb=" N ASN B 799 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 1081 Processing helix chain 'B' and resid 1198 through 1204 Processing helix chain 'B' and resid 1220 through 1224 Processing helix chain 'B' and resid 1231 through 1245 Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 783 through 791 Processing helix chain 'C' and resid 795 through 807 removed outlier: 4.265A pdb=" N ASN C 799 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1081 Processing helix chain 'C' and resid 1198 through 1204 Processing helix chain 'C' and resid 1220 through 1224 Processing helix chain 'C' and resid 1231 through 1245 Processing sheet with id=AA1, first strand: chain 'A' and resid 1097 through 1106 removed outlier: 5.491A pdb=" N HIS A1098 " --> pdb=" O TYR A1117 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR A1117 " --> pdb=" O HIS A1098 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 754 " --> pdb=" O ILE A1120 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE A1122 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A1124 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN A 750 " --> pdb=" O THR A1124 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASN C1180 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 757 " --> pdb=" O ASN C1180 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR C1182 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS A 759 " --> pdb=" O THR C1182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1131 through 1132 removed outlier: 4.238A pdb=" N GLY A1138 " --> pdb=" O MET A1174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1144 through 1149 Processing sheet with id=AA4, first strand: chain 'A' and resid 1180 through 1183 removed outlier: 7.107A pdb=" N GLN B 750 " --> pdb=" O THR B1124 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR B1124 " --> pdb=" O GLN B 750 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE B1122 " --> pdb=" O PRO B 752 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN B 754 " --> pdb=" O ILE B1120 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR B1117 " --> pdb=" O HIS B1098 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS B1098 " --> pdb=" O TYR B1117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1131 through 1132 removed outlier: 4.237A pdb=" N GLY B1138 " --> pdb=" O MET B1174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1144 through 1149 Processing sheet with id=AA7, first strand: chain 'B' and resid 1180 through 1183 removed outlier: 7.107A pdb=" N GLN C 750 " --> pdb=" O THR C1124 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C1124 " --> pdb=" O GLN C 750 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE C1122 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN C 754 " --> pdb=" O ILE C1120 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR C1117 " --> pdb=" O HIS C1098 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N HIS C1098 " --> pdb=" O TYR C1117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1131 through 1132 removed outlier: 4.238A pdb=" N GLY C1138 " --> pdb=" O MET C1174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1144 through 1149 515 hydrogen bonds defined for protein. 1485 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: 2.21 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1541 1.31 - 1.43: 2005 1.43 - 1.56: 4488 1.56 - 1.68: 42 1.68 - 1.81: 48 Bond restraints: 8124 Sorted by residual: bond pdb=" CB HIS A 759 " pdb=" CG HIS A 759 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.11e+01 bond pdb=" CB HIS C 759 " pdb=" CG HIS C 759 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.10e+01 bond pdb=" CB HIS B 759 " pdb=" CG HIS B 759 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.09e+01 bond pdb=" CB PHE C 796 " pdb=" CG PHE C 796 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.05e+01 bond pdb=" CB PHE B 796 " pdb=" CG PHE B 796 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.04e+01 ... (remaining 8119 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.39: 286 106.39 - 113.25: 4171 113.25 - 120.10: 3510 120.10 - 126.96: 3031 126.96 - 133.82: 36 Bond angle restraints: 11034 Sorted by residual: angle pdb=" N TYR B1161 " pdb=" CA TYR B1161 " pdb=" C TYR B1161 " ideal model delta sigma weight residual 108.79 121.68 -12.89 1.53e+00 4.27e-01 7.10e+01 angle pdb=" N TYR A1161 " pdb=" CA TYR A1161 " pdb=" C TYR A1161 " ideal model delta sigma weight residual 108.79 121.66 -12.87 1.53e+00 4.27e-01 7.08e+01 angle pdb=" N TYR C1161 " pdb=" CA TYR C1161 " pdb=" C TYR C1161 " ideal model delta sigma weight residual 108.79 121.62 -12.83 1.53e+00 4.27e-01 7.03e+01 angle pdb=" N ILE C1120 " pdb=" CA ILE C1120 " pdb=" C ILE C1120 " ideal model delta sigma weight residual 113.53 106.94 6.59 9.80e-01 1.04e+00 4.52e+01 angle pdb=" N ILE B1120 " pdb=" CA ILE B1120 " pdb=" C ILE B1120 " ideal model delta sigma weight residual 113.53 106.95 6.58 9.80e-01 1.04e+00 4.50e+01 ... (remaining 11029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 4710 15.46 - 30.91: 144 30.91 - 46.37: 27 46.37 - 61.82: 36 61.82 - 77.28: 18 Dihedral angle restraints: 4935 sinusoidal: 1917 harmonic: 3018 Sorted by residual: dihedral pdb=" CB CYS C 775 " pdb=" SG CYS C 775 " pdb=" SG CYS C 797 " pdb=" CB CYS C 797 " ideal model delta sinusoidal sigma weight residual 93.00 158.77 -65.77 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CB CYS A 775 " pdb=" SG CYS A 775 " pdb=" SG CYS A 797 " pdb=" CB CYS A 797 " ideal model delta sinusoidal sigma weight residual 93.00 158.74 -65.74 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CB CYS B 775 " pdb=" SG CYS B 775 " pdb=" SG CYS B 797 " pdb=" CB CYS B 797 " ideal model delta sinusoidal sigma weight residual 93.00 158.72 -65.72 1 1.00e+01 1.00e-02 5.65e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 704 0.074 - 0.149: 364 0.149 - 0.223: 156 0.223 - 0.297: 39 0.297 - 0.372: 9 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA GLU A1081 " pdb=" N GLU A1081 " pdb=" C GLU A1081 " pdb=" CB GLU A1081 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA LYS B1078 " pdb=" N LYS B1078 " pdb=" C LYS B1078 " pdb=" CB LYS B1078 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA GLU B1081 " pdb=" N GLU B1081 " pdb=" C GLU B1081 " pdb=" CB GLU B1081 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 1269 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1155 " -0.045 2.00e-02 2.50e+03 2.72e-02 1.29e+01 pdb=" CG PHE A1155 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A1155 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A1155 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A1155 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A1155 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A1155 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C1155 " 0.045 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE C1155 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C1155 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C1155 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C1155 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C1155 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C1155 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1155 " 0.045 2.00e-02 2.50e+03 2.70e-02 1.27e+01 pdb=" CG PHE B1155 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B1155 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B1155 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B1155 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B1155 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B1155 " 0.026 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2608 2.81 - 3.33: 8103 3.33 - 3.85: 13493 3.85 - 4.38: 15988 4.38 - 4.90: 25029 Nonbonded interactions: 65221 Sorted by model distance: nonbonded pdb=" OG1 THR A1066 " pdb=" OG SER C1063 " model vdw 2.285 2.440 nonbonded pdb=" OG SER A1063 " pdb=" OG1 THR B1066 " model vdw 2.285 2.440 nonbonded pdb=" OG SER B1063 " pdb=" OG1 THR C1066 " model vdw 2.286 2.440 nonbonded pdb=" N LYS B1154 " pdb=" O LYS B1154 " model vdw 2.396 2.496 nonbonded pdb=" N LYS C1154 " pdb=" O LYS C1154 " model vdw 2.396 2.496 ... (remaining 65216 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' selection = chain 'C' } 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 group one per residue 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.260 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.024 0.146 8124 Z= 1.600 Angle : 1.821 12.890 11034 Z= 1.249 Chirality : 0.105 0.372 1272 Planarity : 0.008 0.033 1446 Dihedral : 10.994 77.281 2943 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.06 % Favored : 97.65 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1020 helix: 1.69 (0.21), residues: 474 sheet: 1.16 (0.42), residues: 129 loop : -0.44 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.013 TRP A1153 HIS 0.014 0.005 HIS B1098 PHE 0.045 0.007 PHE A1155 TYR 0.032 0.007 TYR B1181 ARG 0.008 0.001 ARG C1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 766 THR cc_start: 0.9093 (p) cc_final: 0.8833 (t) REVERT: A 792 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7355 (mt-10) REVERT: A 1153 TRP cc_start: 0.7685 (m100) cc_final: 0.6965 (m100) REVERT: A 1198 ASP cc_start: 0.7796 (t70) cc_final: 0.7427 (m-30) REVERT: B 787 ARG cc_start: 0.5704 (tpp-160) cc_final: 0.5480 (tpt170) REVERT: B 1089 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7619 (mmm-85) REVERT: B 1153 TRP cc_start: 0.7550 (m100) cc_final: 0.7103 (m100) REVERT: B 1223 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7281 (mmmt) REVERT: B 1235 MET cc_start: 0.7751 (mtp) cc_final: 0.7247 (tpp) REVERT: B 1237 ARG cc_start: 0.6565 (mtp180) cc_final: 0.6324 (mmp80) REVERT: C 1188 PHE cc_start: 0.7023 (t80) cc_final: 0.6290 (t80) REVERT: C 1220 ASP cc_start: 0.6912 (t0) cc_final: 0.6697 (t0) REVERT: C 1235 MET cc_start: 0.7888 (mtp) cc_final: 0.6985 (tpp) outliers start: 3 outliers final: 0 residues processed: 223 average time/residue: 0.2249 time to fit residues: 65.4483 Evaluate side-chains 88 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7321 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8124 Z= 0.280 Angle : 0.721 7.994 11034 Z= 0.389 Chirality : 0.044 0.157 1272 Planarity : 0.004 0.031 1446 Dihedral : 5.144 22.877 1089 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.06 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 2.11 (0.25), residues: 1020 helix: 3.49 (0.21), residues: 471 sheet: 0.40 (0.42), residues: 132 loop : -0.83 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1153 HIS 0.004 0.002 HIS A1114 PHE 0.016 0.002 PHE C 796 TYR 0.014 0.002 TYR B1117 ARG 0.006 0.001 ARG B 787 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 766 THR cc_start: 0.9012 (p) cc_final: 0.8697 (t) REVERT: A 767 ARG cc_start: 0.7546 (ptt-90) cc_final: 0.6353 (ptm160) REVERT: A 992 ASN cc_start: 0.7217 (t0) cc_final: 0.6556 (m-40) REVERT: A 1084 LYS cc_start: 0.8673 (mttt) cc_final: 0.8444 (mttt) REVERT: A 1153 TRP cc_start: 0.7551 (m100) cc_final: 0.6671 (m100) REVERT: A 1198 ASP cc_start: 0.7354 (t70) cc_final: 0.6978 (m-30) REVERT: A 1225 ASN cc_start: 0.7321 (m-40) cc_final: 0.6209 (p0) REVERT: A 1233 TYR cc_start: 0.6915 (t80) cc_final: 0.6696 (t80) REVERT: B 792 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6607 (mt-10) REVERT: B 992 ASN cc_start: 0.7272 (t0) cc_final: 0.6477 (m110) REVERT: B 1084 LYS cc_start: 0.8463 (mttt) cc_final: 0.8026 (mttt) REVERT: B 1153 TRP cc_start: 0.7047 (m100) cc_final: 0.6410 (m100) REVERT: B 1188 PHE cc_start: 0.7139 (t80) cc_final: 0.6749 (t80) REVERT: B 1233 TYR cc_start: 0.7188 (t80) cc_final: 0.6912 (t80) REVERT: B 1237 ARG cc_start: 0.6568 (mtp180) cc_final: 0.6097 (mmp80) REVERT: C 992 ASN cc_start: 0.6969 (t0) cc_final: 0.6409 (m-40) REVERT: C 1233 TYR cc_start: 0.7039 (t80) cc_final: 0.6832 (t80) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2101 time to fit residues: 41.3615 Evaluate side-chains 96 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 77 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 92 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.0040 chunk 91 optimal weight: 0.9980 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 GLN A1055 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8124 Z= 0.165 Angle : 0.567 7.870 11034 Z= 0.304 Chirality : 0.039 0.163 1272 Planarity : 0.004 0.028 1446 Dihedral : 4.611 20.362 1089 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.16 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 2.14 (0.26), residues: 1020 helix: 3.56 (0.21), residues: 471 sheet: 0.28 (0.40), residues: 135 loop : -0.83 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1153 HIS 0.002 0.001 HIS A 759 PHE 0.019 0.002 PHE B1207 TYR 0.009 0.001 TYR A1117 ARG 0.003 0.000 ARG C1237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 THR cc_start: 0.8878 (p) cc_final: 0.8580 (t) REVERT: A 767 ARG cc_start: 0.7479 (ptt-90) cc_final: 0.6222 (ptm160) REVERT: A 1084 LYS cc_start: 0.8623 (mttt) cc_final: 0.8391 (mttt) REVERT: A 1153 TRP cc_start: 0.7371 (m100) cc_final: 0.6302 (m100) REVERT: A 1167 THR cc_start: 0.8618 (p) cc_final: 0.8413 (p) REVERT: A 1198 ASP cc_start: 0.7221 (t70) cc_final: 0.6684 (m-30) REVERT: A 1233 TYR cc_start: 0.6945 (t80) cc_final: 0.6729 (t80) REVERT: A 1240 ASP cc_start: 0.7844 (t0) cc_final: 0.7458 (t0) REVERT: B 1084 LYS cc_start: 0.8387 (mttt) cc_final: 0.8045 (mttt) REVERT: B 1146 PHE cc_start: 0.8322 (m-10) cc_final: 0.7811 (m-10) REVERT: B 1153 TRP cc_start: 0.7172 (m100) cc_final: 0.6669 (m100) REVERT: B 1237 ARG cc_start: 0.6645 (mtp180) cc_final: 0.6016 (mmp80) REVERT: C 761 GLU cc_start: 0.7328 (pt0) cc_final: 0.7066 (pm20) REVERT: C 767 ARG cc_start: 0.7515 (ptt-90) cc_final: 0.6637 (ptm160) REVERT: C 992 ASN cc_start: 0.6656 (t0) cc_final: 0.6216 (t0) REVERT: C 1029 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8396 (tm-30) REVERT: C 1153 TRP cc_start: 0.7233 (m100) cc_final: 0.6791 (m100) REVERT: C 1240 ASP cc_start: 0.6421 (t70) cc_final: 0.6211 (t0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2250 time to fit residues: 44.0634 Evaluate side-chains 101 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN B 801 ASN C 801 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8124 Z= 0.338 Angle : 0.707 8.359 11034 Z= 0.378 Chirality : 0.044 0.161 1272 Planarity : 0.004 0.030 1446 Dihedral : 5.265 26.340 1089 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.53 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1020 helix: 2.88 (0.22), residues: 480 sheet: 0.12 (0.43), residues: 108 loop : -1.36 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1206 HIS 0.007 0.002 HIS C1114 PHE 0.021 0.002 PHE B1188 TYR 0.020 0.003 TYR C1181 ARG 0.003 0.001 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 THR cc_start: 0.8766 (p) cc_final: 0.8372 (t) REVERT: A 767 ARG cc_start: 0.8022 (ptt-90) cc_final: 0.6786 (ptm160) REVERT: A 1153 TRP cc_start: 0.7740 (m100) cc_final: 0.6635 (m100) REVERT: A 1198 ASP cc_start: 0.7552 (t70) cc_final: 0.7222 (m-30) REVERT: A 1233 TYR cc_start: 0.6865 (t80) cc_final: 0.6623 (t80) REVERT: B 1084 LYS cc_start: 0.8551 (mttt) cc_final: 0.8264 (mttt) REVERT: B 1153 TRP cc_start: 0.7351 (m100) cc_final: 0.6989 (m100) REVERT: B 1237 ARG cc_start: 0.6517 (mtp180) cc_final: 0.6166 (mmp80) REVERT: B 1240 ASP cc_start: 0.7007 (t70) cc_final: 0.6730 (t0) REVERT: C 1153 TRP cc_start: 0.7514 (m100) cc_final: 0.6861 (m100) REVERT: C 1233 TYR cc_start: 0.6562 (t80) cc_final: 0.6220 (t80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2247 time to fit residues: 41.5487 Evaluate side-chains 90 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN B1055 ASN C1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8124 Z= 0.272 Angle : 0.630 8.291 11034 Z= 0.336 Chirality : 0.041 0.164 1272 Planarity : 0.004 0.029 1446 Dihedral : 5.046 25.299 1089 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.63 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1020 helix: 3.00 (0.22), residues: 471 sheet: -0.33 (0.41), residues: 111 loop : -1.44 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1206 HIS 0.005 0.001 HIS A1114 PHE 0.015 0.002 PHE B 796 TYR 0.016 0.002 TYR C1233 ARG 0.003 0.001 ARG B 787 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 ARG cc_start: 0.7989 (ptt-90) cc_final: 0.6927 (ptm160) REVERT: A 1153 TRP cc_start: 0.7753 (m100) cc_final: 0.6730 (m100) REVERT: B 1077 GLU cc_start: 0.7156 (tt0) cc_final: 0.6356 (tt0) REVERT: B 1084 LYS cc_start: 0.8421 (mttt) cc_final: 0.8032 (mttt) REVERT: B 1237 ARG cc_start: 0.7007 (mtp180) cc_final: 0.6132 (mmp80) REVERT: B 1243 LYS cc_start: 0.8484 (tppt) cc_final: 0.8026 (pttt) REVERT: C 1153 TRP cc_start: 0.7576 (m100) cc_final: 0.6760 (m100) REVERT: C 1171 SER cc_start: 0.8989 (t) cc_final: 0.8751 (m) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2177 time to fit residues: 39.1193 Evaluate side-chains 85 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN B1055 ASN ** C1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8124 Z= 0.202 Angle : 0.564 8.166 11034 Z= 0.301 Chirality : 0.038 0.149 1272 Planarity : 0.004 0.030 1446 Dihedral : 4.734 23.722 1089 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.92 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1020 helix: 3.42 (0.22), residues: 465 sheet: 0.04 (0.37), residues: 117 loop : -1.55 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1206 HIS 0.003 0.001 HIS A1114 PHE 0.015 0.002 PHE B1155 TYR 0.018 0.002 TYR C1233 ARG 0.004 0.000 ARG A1237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 ARG cc_start: 0.8084 (ptt-90) cc_final: 0.6934 (ptm160) REVERT: A 1102 LEU cc_start: 0.8080 (mt) cc_final: 0.7880 (mt) REVERT: A 1153 TRP cc_start: 0.7625 (m100) cc_final: 0.6691 (m100) REVERT: A 1231 LEU cc_start: 0.6790 (mt) cc_final: 0.6179 (mt) REVERT: A 1237 ARG cc_start: 0.7011 (mmp80) cc_final: 0.6543 (mmp80) REVERT: B 1077 GLU cc_start: 0.7021 (tt0) cc_final: 0.6349 (tt0) REVERT: B 1084 LYS cc_start: 0.8360 (mttt) cc_final: 0.8061 (mttt) REVERT: B 1237 ARG cc_start: 0.6960 (mtp180) cc_final: 0.6188 (mmp80) REVERT: B 1243 LYS cc_start: 0.8428 (tppt) cc_final: 0.8013 (pttt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2457 time to fit residues: 41.8378 Evaluate side-chains 87 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 ASN B1055 ASN C 992 ASN ** C1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8124 Z= 0.261 Angle : 0.615 8.078 11034 Z= 0.326 Chirality : 0.041 0.145 1272 Planarity : 0.004 0.031 1446 Dihedral : 4.953 23.524 1089 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.12 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1020 helix: 2.96 (0.23), residues: 486 sheet: -0.71 (0.37), residues: 144 loop : -1.67 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1206 HIS 0.006 0.001 HIS A1114 PHE 0.018 0.002 PHE B1155 TYR 0.015 0.002 TYR C1181 ARG 0.003 0.001 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 ARG cc_start: 0.8131 (ptt-90) cc_final: 0.7050 (ptm160) REVERT: A 1092 PHE cc_start: 0.8579 (t80) cc_final: 0.8350 (t80) REVERT: A 1153 TRP cc_start: 0.7617 (m100) cc_final: 0.6692 (m100) REVERT: A 1231 LEU cc_start: 0.7062 (mt) cc_final: 0.6733 (mt) REVERT: A 1237 ARG cc_start: 0.7056 (mmp80) cc_final: 0.6455 (mmp80) REVERT: B 992 ASN cc_start: 0.7523 (t0) cc_final: 0.7254 (m110) REVERT: B 1084 LYS cc_start: 0.8381 (mttt) cc_final: 0.8072 (mttt) REVERT: B 1237 ARG cc_start: 0.6514 (mtp180) cc_final: 0.6039 (mmp80) REVERT: B 1240 ASP cc_start: 0.7800 (t0) cc_final: 0.7403 (t0) REVERT: C 1092 PHE cc_start: 0.8534 (t80) cc_final: 0.8113 (t80) REVERT: C 1102 LEU cc_start: 0.7943 (mt) cc_final: 0.7688 (mt) REVERT: C 1113 ILE cc_start: 0.7606 (pt) cc_final: 0.7373 (tp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2118 time to fit residues: 34.5030 Evaluate side-chains 86 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 ASN B 750 GLN ** B1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 ASN C1055 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8124 Z= 0.230 Angle : 0.592 7.913 11034 Z= 0.313 Chirality : 0.040 0.136 1272 Planarity : 0.004 0.032 1446 Dihedral : 4.845 22.946 1089 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.73 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1020 helix: 3.09 (0.23), residues: 483 sheet: -0.85 (0.39), residues: 141 loop : -1.70 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1206 HIS 0.004 0.001 HIS A1114 PHE 0.017 0.002 PHE B1155 TYR 0.012 0.002 TYR C1117 ARG 0.003 0.001 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 ARG cc_start: 0.8081 (ptt-90) cc_final: 0.6980 (ptm160) REVERT: A 1092 PHE cc_start: 0.8564 (t80) cc_final: 0.8349 (t80) REVERT: A 1183 LYS cc_start: 0.8166 (tttt) cc_final: 0.7939 (tttm) REVERT: A 1237 ARG cc_start: 0.6888 (mmp80) cc_final: 0.6676 (mmp80) REVERT: B 1084 LYS cc_start: 0.8387 (mttt) cc_final: 0.8087 (mttt) REVERT: B 1237 ARG cc_start: 0.6523 (mtp180) cc_final: 0.5946 (mmp80) REVERT: B 1243 LYS cc_start: 0.8233 (tppt) cc_final: 0.7937 (mttm) REVERT: C 1092 PHE cc_start: 0.8447 (t80) cc_final: 0.8063 (t80) REVERT: C 1102 LEU cc_start: 0.7958 (mt) cc_final: 0.7684 (mt) REVERT: C 1113 ILE cc_start: 0.7635 (pt) cc_final: 0.7337 (tp) REVERT: C 1237 ARG cc_start: 0.6336 (mmp80) cc_final: 0.5945 (mmp80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2236 time to fit residues: 35.7879 Evaluate side-chains 96 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.0060 chunk 60 optimal weight: 0.0570 chunk 96 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1055 ASN C 750 GLN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8124 Z= 0.155 Angle : 0.543 9.328 11034 Z= 0.283 Chirality : 0.038 0.132 1272 Planarity : 0.004 0.032 1446 Dihedral : 4.488 22.055 1089 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.33 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 1020 helix: 3.44 (0.23), residues: 480 sheet: -0.40 (0.40), residues: 138 loop : -1.66 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1153 HIS 0.004 0.001 HIS C 759 PHE 0.012 0.002 PHE A1115 TYR 0.019 0.001 TYR A1233 ARG 0.004 0.000 ARG C1237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 ARG cc_start: 0.7973 (ptt-90) cc_final: 0.6848 (ptm160) REVERT: A 1092 PHE cc_start: 0.8469 (t80) cc_final: 0.8217 (t80) REVERT: A 1153 TRP cc_start: 0.7397 (m100) cc_final: 0.6294 (m100) REVERT: A 1174 MET cc_start: 0.5692 (mmm) cc_final: 0.4957 (mmm) REVERT: A 1243 LYS cc_start: 0.8691 (tptt) cc_final: 0.8461 (mttp) REVERT: B 1084 LYS cc_start: 0.8279 (mttt) cc_final: 0.8001 (mttt) REVERT: B 1234 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 1237 ARG cc_start: 0.6432 (mtp180) cc_final: 0.5979 (mmp80) REVERT: B 1243 LYS cc_start: 0.8341 (tppt) cc_final: 0.7988 (mttm) REVERT: C 1092 PHE cc_start: 0.8356 (t80) cc_final: 0.7978 (t80) REVERT: C 1237 ARG cc_start: 0.6483 (mmp80) cc_final: 0.6107 (mmp80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2171 time to fit residues: 36.3683 Evaluate side-chains 93 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8124 Z= 0.313 Angle : 0.674 9.747 11034 Z= 0.353 Chirality : 0.043 0.140 1272 Planarity : 0.004 0.033 1446 Dihedral : 5.019 23.599 1089 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.22 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.96 (0.26), residues: 1020 helix: 2.97 (0.23), residues: 477 sheet: -1.01 (0.40), residues: 141 loop : -1.78 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1153 HIS 0.007 0.002 HIS A1114 PHE 0.021 0.002 PHE C1155 TYR 0.016 0.002 TYR C1117 ARG 0.003 0.001 ARG A1089 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 ARG cc_start: 0.8131 (ptt-90) cc_final: 0.6961 (ptm160) REVERT: A 1237 ARG cc_start: 0.6538 (mmp80) cc_final: 0.6171 (mmp80) REVERT: A 1243 LYS cc_start: 0.8739 (tptt) cc_final: 0.8492 (mttp) REVERT: B 1077 GLU cc_start: 0.7322 (tt0) cc_final: 0.6831 (tt0) REVERT: B 1084 LYS cc_start: 0.8286 (mttt) cc_final: 0.7986 (mttt) REVERT: B 1234 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 1243 LYS cc_start: 0.8411 (tppt) cc_final: 0.8019 (mttm) REVERT: C 1092 PHE cc_start: 0.8453 (t80) cc_final: 0.8079 (t80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2137 time to fit residues: 33.8784 Evaluate side-chains 92 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 ASN C 992 ASN ** C1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.152297 restraints weight = 9737.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139422 restraints weight = 14480.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138478 restraints weight = 14555.126| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8124 Z= 0.234 Angle : 0.604 10.035 11034 Z= 0.315 Chirality : 0.040 0.137 1272 Planarity : 0.004 0.034 1446 Dihedral : 4.785 22.273 1089 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.02 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1020 helix: 3.07 (0.23), residues: 483 sheet: -1.02 (0.40), residues: 141 loop : -1.81 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1153 HIS 0.005 0.001 HIS A1114 PHE 0.021 0.002 PHE A1092 TYR 0.018 0.002 TYR A1233 ARG 0.004 0.001 ARG A1089 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.67 seconds wall clock time: 34 minutes 12.74 seconds (2052.74 seconds total)