Starting phenix.real_space_refine on Tue Nov 14 22:15:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/11_2023/7bzw_30261.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/11_2023/7bzw_30261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/11_2023/7bzw_30261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/11_2023/7bzw_30261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/11_2023/7bzw_30261.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/11_2023/7bzw_30261.pdb" } resolution = 4.6 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= 0.003 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 6120 2.51 5 N 1656 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ASP 130": "OD1" <-> "OD2" Residue "1 GLU 137": "OE1" <-> "OE2" Residue "1 GLU 166": "OE1" <-> "OE2" Residue "1 GLU 170": "OE1" <-> "OE2" Residue "1 ASP 174": "OD1" <-> "OD2" Residue "1 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 223": "OD1" <-> "OD2" Residue "2 ASP 130": "OD1" <-> "OD2" Residue "2 GLU 137": "OE1" <-> "OE2" Residue "2 GLU 166": "OE1" <-> "OE2" Residue "2 GLU 170": "OE1" <-> "OE2" Residue "2 ASP 174": "OD1" <-> "OD2" Residue "2 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 223": "OD1" <-> "OD2" Residue "3 ASP 130": "OD1" <-> "OD2" Residue "3 GLU 137": "OE1" <-> "OE2" Residue "3 GLU 166": "OE1" <-> "OE2" Residue "3 GLU 170": "OE1" <-> "OE2" Residue "3 ASP 174": "OD1" <-> "OD2" Residue "3 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 223": "OD1" <-> "OD2" Residue "4 ASP 130": "OD1" <-> "OD2" Residue "4 GLU 137": "OE1" <-> "OE2" Residue "4 GLU 166": "OE1" <-> "OE2" Residue "4 GLU 170": "OE1" <-> "OE2" Residue "4 ASP 174": "OD1" <-> "OD2" Residue "4 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 223": "OD1" <-> "OD2" Residue "5 ASP 130": "OD1" <-> "OD2" Residue "5 GLU 137": "OE1" <-> "OE2" Residue "5 GLU 166": "OE1" <-> "OE2" Residue "5 GLU 170": "OE1" <-> "OE2" Residue "5 ASP 174": "OD1" <-> "OD2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 223": "OD1" <-> "OD2" Residue "6 ASP 130": "OD1" <-> "OD2" Residue "6 GLU 137": "OE1" <-> "OE2" Residue "6 GLU 166": "OE1" <-> "OE2" Residue "6 GLU 170": "OE1" <-> "OE2" Residue "6 ASP 174": "OD1" <-> "OD2" Residue "6 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 223": "OD1" <-> "OD2" Residue "7 ASP 130": "OD1" <-> "OD2" Residue "7 GLU 137": "OE1" <-> "OE2" Residue "7 GLU 166": "OE1" <-> "OE2" Residue "7 GLU 170": "OE1" <-> "OE2" Residue "7 ASP 174": "OD1" <-> "OD2" Residue "7 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 223": "OD1" <-> "OD2" Residue "8 ASP 130": "OD1" <-> "OD2" Residue "8 GLU 137": "OE1" <-> "OE2" Residue "8 GLU 166": "OE1" <-> "OE2" Residue "8 GLU 170": "OE1" <-> "OE2" Residue "8 ASP 174": "OD1" <-> "OD2" Residue "8 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 223": "OD1" <-> "OD2" Residue "9 ASP 130": "OD1" <-> "OD2" Residue "9 GLU 137": "OE1" <-> "OE2" Residue "9 GLU 166": "OE1" <-> "OE2" Residue "9 GLU 170": "OE1" <-> "OE2" Residue "9 ASP 174": "OD1" <-> "OD2" Residue "9 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 223": "OD1" <-> "OD2" Residue "10 ASP 130": "OD1" <-> "OD2" Residue "10 GLU 137": "OE1" <-> "OE2" Residue "10 GLU 166": "OE1" <-> "OE2" Residue "10 GLU 170": "OE1" <-> "OE2" Residue "10 ASP 174": "OD1" <-> "OD2" Residue "10 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 ASP 223": "OD1" <-> "OD2" Residue "11 ASP 130": "OD1" <-> "OD2" Residue "11 GLU 137": "OE1" <-> "OE2" Residue "11 GLU 166": "OE1" <-> "OE2" Residue "11 GLU 170": "OE1" <-> "OE2" Residue "11 ASP 174": "OD1" <-> "OD2" Residue "11 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "11 ASP 223": "OD1" <-> "OD2" Residue "12 ASP 130": "OD1" <-> "OD2" Residue "12 GLU 137": "OE1" <-> "OE2" Residue "12 GLU 166": "OE1" <-> "OE2" Residue "12 GLU 170": "OE1" <-> "OE2" Residue "12 ASP 174": "OD1" <-> "OD2" Residue "12 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ASP 223": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9756 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "2" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "3" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "4" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "5" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "6" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "7" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "8" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "9" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "10" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "11" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "12" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 5.11, per 1000 atoms: 0.52 Number of scatterers: 9756 At special positions: 0 Unit cell: (113.42, 114.48, 104.94, 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 1944 8.00 N 1656 7.00 C 6120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 1.6 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '1' and resid 130 through 133 Processing sheet with id=AA2, first strand: chain '1' and resid 152 through 155 Processing sheet with id=AA3, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AA4, first strand: chain '2' and resid 152 through 155 Processing sheet with id=AA5, first strand: chain '3' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain '3' and resid 152 through 155 Processing sheet with id=AA7, first strand: chain '4' and resid 130 through 133 Processing sheet with id=AA8, first strand: chain '4' and resid 152 through 155 Processing sheet with id=AA9, first strand: chain '5' and resid 130 through 133 Processing sheet with id=AB1, first strand: chain '5' and resid 152 through 155 Processing sheet with id=AB2, first strand: chain '6' and resid 130 through 133 Processing sheet with id=AB3, first strand: chain '6' and resid 152 through 155 Processing sheet with id=AB4, first strand: chain '7' and resid 130 through 133 Processing sheet with id=AB5, first strand: chain '7' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain '8' and resid 130 through 133 Processing sheet with id=AB7, first strand: chain '8' and resid 152 through 155 Processing sheet with id=AB8, first strand: chain '9' and resid 130 through 133 Processing sheet with id=AB9, first strand: chain '9' and resid 152 through 155 Processing sheet with id=AC1, first strand: chain '10' and resid 130 through 133 Processing sheet with id=AC2, first strand: chain '10' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain '11' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain '11' and resid 152 through 155 Processing sheet with id=AC5, first strand: chain '12' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain '12' and resid 152 through 155 288 hydrogen bonds defined for protein. 720 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: 2.10 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3252 1.34 - 1.46: 1639 1.46 - 1.58: 4937 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 9888 Sorted by residual: bond pdb=" CA GLY 4 165 " pdb=" C GLY 4 165 " ideal model delta sigma weight residual 1.516 1.509 0.007 1.01e-02 9.80e+03 4.95e-01 bond pdb=" N LYS11 216 " pdb=" CA LYS11 216 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.86e-01 bond pdb=" N GLY 6 165 " pdb=" CA GLY 6 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.84e-01 bond pdb=" N GLY12 165 " pdb=" CA GLY12 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.82e-01 bond pdb=" N GLY 7 165 " pdb=" CA GLY 7 165 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.16e-02 7.43e+03 4.74e-01 ... (remaining 9883 not shown) Histogram of bond angle deviations from ideal: 101.27 - 107.81: 394 107.81 - 114.34: 5896 114.34 - 120.88: 3566 120.88 - 127.41: 3320 127.41 - 133.95: 84 Bond angle restraints: 13260 Sorted by residual: angle pdb=" C ILE 6 131 " pdb=" N LYS 6 132 " pdb=" CA LYS 6 132 " ideal model delta sigma weight residual 121.63 117.02 4.61 1.92e+00 2.71e-01 5.78e+00 angle pdb=" C ILE 2 131 " pdb=" N LYS 2 132 " pdb=" CA LYS 2 132 " ideal model delta sigma weight residual 121.63 117.03 4.60 1.92e+00 2.71e-01 5.73e+00 angle pdb=" C ILE 8 131 " pdb=" N LYS 8 132 " pdb=" CA LYS 8 132 " ideal model delta sigma weight residual 121.63 117.04 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C ILE10 131 " pdb=" N LYS10 132 " pdb=" CA LYS10 132 " ideal model delta sigma weight residual 121.63 117.04 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C ILE 7 131 " pdb=" N LYS 7 132 " pdb=" CA LYS 7 132 " ideal model delta sigma weight residual 121.63 117.05 4.58 1.92e+00 2.71e-01 5.69e+00 ... (remaining 13255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.42: 4716 11.42 - 22.84: 935 22.84 - 34.26: 469 34.26 - 45.67: 72 45.67 - 57.09: 60 Dihedral angle restraints: 6252 sinusoidal: 2736 harmonic: 3516 Sorted by residual: dihedral pdb=" CA GLU 9 195 " pdb=" C GLU 9 195 " pdb=" N LYS 9 196 " pdb=" CA LYS 9 196 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU 4 195 " pdb=" C GLU 4 195 " pdb=" N LYS 4 196 " pdb=" CA LYS 4 196 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU 5 195 " pdb=" C GLU 5 195 " pdb=" N LYS 5 196 " pdb=" CA LYS 5 196 " ideal model delta harmonic sigma weight residual 180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 650 0.028 - 0.056: 426 0.056 - 0.085: 229 0.085 - 0.113: 89 0.113 - 0.141: 82 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA ILE 3 138 " pdb=" N ILE 3 138 " pdb=" C ILE 3 138 " pdb=" CB ILE 3 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE 8 138 " pdb=" N ILE 8 138 " pdb=" C ILE 8 138 " pdb=" CB ILE 8 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE 6 138 " pdb=" N ILE 6 138 " pdb=" C ILE 6 138 " pdb=" CB ILE 6 138 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1473 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 4 190 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO 4 191 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO 4 191 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 4 191 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 190 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO 2 191 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO 2 191 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 2 191 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 5 190 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO 5 191 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO 5 191 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 5 191 " -0.029 5.00e-02 4.00e+02 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 740 2.72 - 3.27: 10669 3.27 - 3.81: 15449 3.81 - 4.36: 18051 4.36 - 4.90: 28123 Nonbonded interactions: 73032 Sorted by model distance: nonbonded pdb=" OE1 GLN 9 167 " pdb=" OH TYR 9 184 " model vdw 2.176 2.440 nonbonded pdb=" OE1 GLN 5 167 " pdb=" OH TYR 5 184 " model vdw 2.176 2.440 nonbonded pdb=" OE1 GLN 3 167 " pdb=" OH TYR 3 184 " model vdw 2.176 2.440 nonbonded pdb=" OE1 GLN11 167 " pdb=" OH TYR11 184 " model vdw 2.176 2.440 nonbonded pdb=" OE1 GLN 4 167 " pdb=" OH TYR 4 184 " model vdw 2.176 2.440 ... (remaining 73027 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 '1' selection = chain '10' selection = chain '11' selection = chain '12' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain '1' selection = chain '10' selection = chain '11' selection = chain '12' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } Set refine NCS operators NCS operators will be refined. 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: 0.810 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: 3.350 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.760 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9888 Z= 0.227 Angle : 0.823 4.614 13260 Z= 0.458 Chirality : 0.054 0.141 1476 Planarity : 0.006 0.053 1704 Dihedral : 15.818 57.093 3948 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.36 % Favored : 80.64 % Rotamer: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % 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: -5.59 (0.20), residues: 1188 helix: -5.58 (0.06), residues: 72 sheet: -3.01 (0.21), residues: 420 loop : -4.13 (0.20), residues: 696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1981 time to fit residues: 6.9400 Evaluate side-chains 18 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 0.0570 chunk 94 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9888 Z= 0.230 Angle : 0.760 4.171 13260 Z= 0.403 Chirality : 0.054 0.167 1476 Planarity : 0.005 0.049 1704 Dihedral : 7.224 28.547 1260 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -2.05 (0.21), residues: 456 loop : -3.83 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1960 time to fit residues: 5.2393 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 0.0370 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9888 Z= 0.264 Angle : 0.764 5.048 13260 Z= 0.404 Chirality : 0.056 0.189 1476 Planarity : 0.005 0.051 1704 Dihedral : 6.979 26.966 1260 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 1.06 % Allowed : 9.57 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -1.97 (0.21), residues: 456 loop : -3.74 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.104 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1636 time to fit residues: 4.4212 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.096 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 0.0970 chunk 109 optimal weight: 0.2980 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 0.0980 chunk 103 optimal weight: 0.0370 chunk 31 optimal weight: 10.0000 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9888 Z= 0.225 Angle : 0.742 5.132 13260 Z= 0.392 Chirality : 0.052 0.196 1476 Planarity : 0.005 0.048 1704 Dihedral : 6.919 22.281 1260 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.21), residues: 1188 helix: None (None), residues: 0 sheet: -1.25 (0.21), residues: 432 loop : -3.57 (0.20), residues: 756 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1380 time to fit residues: 3.2211 Evaluate side-chains 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0970 chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.0040 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9888 Z= 0.201 Angle : 0.703 4.737 13260 Z= 0.363 Chirality : 0.050 0.145 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.449 18.658 1260 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -1.03 (0.20), residues: 492 loop : -3.57 (0.21), residues: 696 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.104 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1088 time to fit residues: 2.7127 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 116 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.0770 chunk 60 optimal weight: 8.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 9888 Z= 0.184 Angle : 0.684 4.249 13260 Z= 0.355 Chirality : 0.052 0.163 1476 Planarity : 0.005 0.044 1704 Dihedral : 5.864 16.931 1260 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.74 (0.21), residues: 492 loop : -3.40 (0.21), residues: 696 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.103 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1197 time to fit residues: 2.5655 Evaluate side-chains 13 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9888 Z= 0.186 Angle : 0.679 4.387 13260 Z= 0.354 Chirality : 0.049 0.138 1476 Planarity : 0.005 0.043 1704 Dihedral : 6.064 18.423 1260 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.21), residues: 1188 helix: None (None), residues: 0 sheet: -1.07 (0.20), residues: 492 loop : -3.43 (0.21), residues: 696 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.113 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0687 time to fit residues: 1.6224 Evaluate side-chains 13 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.0040 chunk 69 optimal weight: 0.0010 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.0470 chunk 57 optimal weight: 0.0040 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.8005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 9888 Z= 0.181 Angle : 0.735 5.683 13260 Z= 0.376 Chirality : 0.055 0.215 1476 Planarity : 0.005 0.046 1704 Dihedral : 5.810 16.941 1260 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -2.93 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.58 (0.19), residues: 432 loop : -2.98 (0.22), residues: 756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.110 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0708 time to fit residues: 1.5791 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.0030 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 0.0040 chunk 84 optimal weight: 0.0980 chunk 33 optimal weight: 0.0670 chunk 97 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 0.0020 chunk 69 optimal weight: 3.9990 overall best weight: 0.0348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.8753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9888 Z= 0.207 Angle : 0.857 6.567 13260 Z= 0.445 Chirality : 0.060 0.236 1476 Planarity : 0.006 0.045 1704 Dihedral : 5.971 18.214 1260 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.21 % Favored : 78.79 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.65 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.55 (0.20), residues: 492 loop : -2.84 (0.24), residues: 696 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.103 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0635 time to fit residues: 1.2749 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 0.0870 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.0770 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.8637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9888 Z= 0.200 Angle : 0.747 4.983 13260 Z= 0.401 Chirality : 0.057 0.197 1476 Planarity : 0.006 0.045 1704 Dihedral : 5.765 17.268 1260 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.21 % Favored : 78.79 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.39 (0.24), residues: 1188 helix: None (None), residues: 0 sheet: -0.31 (0.21), residues: 492 loop : -2.70 (0.24), residues: 696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.099 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0699 time to fit residues: 1.4111 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 0.0030 chunk 97 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034161 restraints weight = 8993.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.034704 restraints weight = 7336.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035087 restraints weight = 6356.427| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.8656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9888 Z= 0.182 Angle : 0.736 5.506 13260 Z= 0.379 Chirality : 0.054 0.176 1476 Planarity : 0.006 0.045 1704 Dihedral : 5.583 18.060 1260 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.79 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.71 (0.20), residues: 492 loop : -2.87 (0.23), residues: 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.94 seconds wall clock time: 34 minutes 36.72 seconds (2076.72 seconds total)