Starting phenix.real_space_refine (version: dev) on Sat Feb 18 10:08:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/02_2023/6b3o_7040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/02_2023/6b3o_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_7040/02_2023/6b3o_7040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/02_2023/6b3o_7040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/02_2023/6b3o_7040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3o_7040/02_2023/6b3o_7040.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.13, per 1000 atoms: 0.64 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: 3.43 Conformation dependent library (CDL) restraints added in 1.2 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: 0.35 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: 2.34 Time building geometry restraints manager: 3.67 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 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. 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: 1.720 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: 7.180 Check model and map are aligned: 0.120 Process input model: 25.280 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 % 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 *********************** 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 : 1.060 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 223 average time/residue: 0.2277 time to fit residues: 66.4986 Evaluate side-chains 82 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2589 ------------------------------------------------------------------------------- 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: 0.5980 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 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: 0.7980 chunk 92 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 8124 Z= 0.283 Angle : 0.727 8.020 11034 Z= 0.392 Chirality : 0.044 0.185 1272 Planarity : 0.004 0.034 1446 Dihedral : 5.139 22.813 1089 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.67 % Favored : 98.04 % Rotamer Outliers : 0.00 % 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: 2.09 (0.25), residues: 1020 helix: 3.44 (0.21), residues: 471 sheet: 0.42 (0.42), residues: 132 loop : -0.81 (0.28), residues: 417 *********************** 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 143 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2109 time to fit residues: 40.5608 Evaluate side-chains 96 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2778 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 63 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 82 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8124 Z= 0.218 Angle : 0.600 8.065 11034 Z= 0.321 Chirality : 0.040 0.152 1272 Planarity : 0.004 0.028 1446 Dihedral : 4.755 22.783 1089 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.55 % Favored : 97.16 % Rotamer Outliers : 0.00 % 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: 2.01 (0.26), residues: 1020 helix: 3.54 (0.21), residues: 471 sheet: 0.31 (0.41), residues: 129 loop : -1.04 (0.28), residues: 420 *********************** 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 142 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2157 time to fit residues: 41.4098 Evaluate side-chains 87 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4598 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 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 750 GLN A 801 ASN A1011 ASN B 801 ASN C 788 GLN C 801 ASN C1170 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 8124 Z= 0.345 Angle : 0.714 8.364 11034 Z= 0.380 Chirality : 0.044 0.160 1272 Planarity : 0.004 0.031 1446 Dihedral : 5.329 26.162 1089 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.53 % Favored : 96.18 % Rotamer Outliers : 0.11 % 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 (0.25), residues: 1020 helix: 2.91 (0.21), residues: 480 sheet: -0.03 (0.42), residues: 108 loop : -1.50 (0.26), residues: 432 *********************** 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 125 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2006 time to fit residues: 34.5897 Evaluate side-chains 82 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4924 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 ASN C1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5129 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= 0.282 Angle : 0.631 8.205 11034 Z= 0.338 Chirality : 0.041 0.147 1272 Planarity : 0.004 0.030 1446 Dihedral : 5.178 25.393 1089 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.73 % Favored : 95.98 % Rotamer Outliers : 0.00 % 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 (0.25), residues: 1020 helix: 3.02 (0.22), residues: 474 sheet: -0.20 (0.42), residues: 108 loop : -1.70 (0.25), residues: 438 *********************** 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 127 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2005 time to fit residues: 35.2500 Evaluate side-chains 82 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2609 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1055 ASN C 992 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: 0.7633 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8124 Z= 0.285 Angle : 0.637 8.151 11034 Z= 0.338 Chirality : 0.041 0.157 1272 Planarity : 0.004 0.031 1446 Dihedral : 5.133 24.241 1089 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.92 % Favored : 95.78 % Rotamer Outliers : 0.00 % 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: 0.98 (0.25), residues: 1020 helix: 2.89 (0.22), residues: 480 sheet: -0.32 (0.43), residues: 108 loop : -1.85 (0.25), residues: 432 *********************** 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 118 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.890 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 outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1935 time to fit residues: 32.0051 Evaluate side-chains 85 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2704 ------------------------------------------------------------------------------- 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: 0.6980 chunk 83 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** B1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8124 Z= 0.274 Angle : 0.624 8.160 11034 Z= 0.332 Chirality : 0.041 0.146 1272 Planarity : 0.004 0.032 1446 Dihedral : 5.134 23.724 1089 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.63 % Favored : 96.08 % Rotamer Outliers : 0.00 % 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: 0.98 (0.26), residues: 1020 helix: 2.89 (0.22), residues: 486 sheet: -0.37 (0.44), residues: 108 loop : -1.91 (0.25), residues: 426 *********************** 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 123 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2086 time to fit residues: 35.2336 Evaluate side-chains 79 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4066 ------------------------------------------------------------------------------- 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: 0.8980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 ASN B1055 ASN ** 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: 0.7656 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 8124 Z= 0.309 Angle : 0.657 8.023 11034 Z= 0.349 Chirality : 0.042 0.140 1272 Planarity : 0.004 0.032 1446 Dihedral : 5.335 23.640 1089 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.82 % Favored : 95.88 % Rotamer Outliers : 0.00 % 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: 0.82 (0.26), residues: 1020 helix: 2.74 (0.23), residues: 483 sheet: -0.73 (0.44), residues: 111 loop : -1.85 (0.25), residues: 426 *********************** 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 122 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2161 time to fit residues: 35.9322 Evaluate side-chains 81 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2046 ------------------------------------------------------------------------------- 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: 0.3980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 ASN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5885 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= 0.218 Angle : 0.588 7.723 11034 Z= 0.310 Chirality : 0.040 0.141 1272 Planarity : 0.004 0.034 1446 Dihedral : 5.000 22.811 1089 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.73 % Favored : 95.98 % Rotamer Outliers : 0.00 % 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: 0.99 (0.26), residues: 1020 helix: 2.91 (0.23), residues: 489 sheet: -0.67 (0.44), residues: 111 loop : -1.86 (0.25), residues: 420 *********************** 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 128 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2145 time to fit residues: 37.2588 Evaluate side-chains 81 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2083 ------------------------------------------------------------------------------- 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: 5.9990 chunk 93 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** B1055 ASN C 750 GLN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8124 Z= 0.249 Angle : 0.621 9.303 11034 Z= 0.325 Chirality : 0.041 0.141 1272 Planarity : 0.004 0.037 1446 Dihedral : 5.024 23.279 1089 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.12 % Favored : 95.59 % Rotamer Outliers : 0.00 % 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: 0.89 (0.26), residues: 1020 helix: 2.87 (0.23), residues: 489 sheet: -0.81 (0.44), residues: 108 loop : -1.94 (0.25), residues: 423 ********************** 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 116 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2244 time to fit residues: 35.2570 Evaluate side-chains 79 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3005 ------------------------------------------------------------------------------- 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: 2.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149819 restraints weight = 9924.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135749 restraints weight = 15554.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135751 restraints weight = 13550.798| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 8124 Z= 0.297 Angle : 0.655 10.008 11034 Z= 0.345 Chirality : 0.042 0.148 1272 Planarity : 0.004 0.040 1446 Dihedral : 5.253 25.910 1089 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.71 % Favored : 95.00 % Rotamer Outliers : 0.00 % 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: 0.76 (0.26), residues: 1020 helix: 2.73 (0.23), residues: 489 sheet: -1.09 (0.43), residues: 111 loop : -1.89 (0.25), residues: 420 =============================================================================== Job complete usr+sys time: 1707.73 seconds wall clock time: 32 minutes 13.80 seconds (1933.80 seconds total)