Starting phenix.real_space_refine on Thu Mar 14 21:04:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/03_2024/7bzw_30261.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/03_2024/7bzw_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_30261/03_2024/7bzw_30261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/03_2024/7bzw_30261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/03_2024/7bzw_30261.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzw_30261/03_2024/7bzw_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-dev-5265/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: 5.52, per 1000 atoms: 0.57 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: 4.22 Conformation dependent library (CDL) restraints added in 1.8 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: 1.09 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: 2.25 Time building geometry restraints manager: 4.53 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: 0.610 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: 3.320 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 29.040 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP10 129 HIS 0.001 0.000 HIS 4 136 PHE 0.005 0.001 PHE 5 142 TYR 0.009 0.003 TYR11 184 ARG 0.003 0.000 ARG 6 187 *********************** 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 : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 217 VAL cc_start: 0.8057 (t) cc_final: 0.7734 (p) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2062 time to fit residues: 7.2054 Evaluate side-chains 18 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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: 0.7000 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9888 Z= 0.241 Angle : 0.754 4.245 13260 Z= 0.401 Chirality : 0.053 0.172 1476 Planarity : 0.005 0.050 1704 Dihedral : 7.221 28.664 1260 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.21 % Favored : 78.79 % 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: -4.47 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -2.04 (0.21), residues: 456 loop : -3.81 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 3 176 HIS 0.000 0.000 HIS 1 136 PHE 0.010 0.003 PHE 7 142 TYR 0.008 0.004 TYR12 184 ARG 0.002 0.001 ARG 7 187 *********************** 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 : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 9 196 LYS cc_start: 0.5780 (tttt) cc_final: 0.5516 (tptt) REVERT: 9 217 VAL cc_start: 0.7844 (t) cc_final: 0.7124 (p) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2088 time to fit residues: 5.5901 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 109 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 108 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- 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: 0.6996 moved from start: 0.4778 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= 0.212 Angle : 0.690 5.359 13260 Z= 0.366 Chirality : 0.052 0.185 1476 Planarity : 0.005 0.048 1704 Dihedral : 6.503 23.257 1260 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % 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: -4.07 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -1.63 (0.23), residues: 456 loop : -3.64 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 9 176 HIS 0.000 0.000 HIS 1 136 PHE 0.011 0.003 PHE 7 142 TYR 0.001 0.001 TYR 8 184 ARG 0.002 0.001 ARG 1 187 *********************** 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 24 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 197 ASP cc_start: 0.8075 (p0) cc_final: 0.7733 (p0) REVERT: 8 217 VAL cc_start: 0.7963 (t) cc_final: 0.7589 (p) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1699 time to fit residues: 4.4165 Evaluate side-chains 17 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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: 0.0570 chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 0.0040 chunk 109 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 57 optimal weight: 0.0020 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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: 0.6881 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9888 Z= 0.234 Angle : 0.734 5.841 13260 Z= 0.392 Chirality : 0.052 0.213 1476 Planarity : 0.005 0.045 1704 Dihedral : 6.723 20.920 1260 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % 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: -3.65 (0.21), residues: 1188 helix: None (None), residues: 0 sheet: -0.85 (0.20), residues: 432 loop : -3.66 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 176 HIS 0.002 0.001 HIS 8 136 PHE 0.010 0.003 PHE 4 142 TYR 0.007 0.002 TYR 6 184 ARG 0.001 0.000 ARG 6 187 *********************** REFINEMENT MACRO_CYCLE 4 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 19 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 197 ASP cc_start: 0.8134 (p0) cc_final: 0.7729 (p0) REVERT: 8 210 ILE cc_start: 0.7902 (mp) cc_final: 0.6767 (mp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1466 time to fit residues: 3.0738 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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: 0.7980 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 86 optimal weight: 0.1980 chunk 47 optimal weight: 0.0050 chunk 98 optimal weight: 0.1980 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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: 0.6863 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9888 Z= 0.181 Angle : 0.652 3.818 13260 Z= 0.346 Chirality : 0.050 0.147 1476 Planarity : 0.005 0.043 1704 Dihedral : 6.202 17.784 1260 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.51 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: -3.31 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -0.51 (0.21), residues: 432 loop : -3.50 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP10 129 HIS 0.001 0.000 HIS 1 136 PHE 0.009 0.003 PHE 6 142 TYR 0.006 0.002 TYR 6 184 ARG 0.002 0.001 ARG 2 141 *********************** 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 : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 11 223 ASP cc_start: 0.5902 (t0) cc_final: 0.5613 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1051 time to fit residues: 2.6231 Evaluate side-chains 17 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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: 0.9980 chunk 104 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 0.0050 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 0.0070 chunk 38 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 overall best weight: 0.3812 ------------------------------------------------------------------------------- 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: 0.6771 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9888 Z= 0.194 Angle : 0.682 5.543 13260 Z= 0.355 Chirality : 0.052 0.198 1476 Planarity : 0.005 0.042 1704 Dihedral : 5.839 19.665 1260 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.17 % Favored : 82.83 % 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: -3.13 (0.23), residues: 1188 helix: None (None), residues: 0 sheet: -0.26 (0.22), residues: 432 loop : -3.46 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 4 176 HIS 0.003 0.002 HIS 1 136 PHE 0.014 0.003 PHE 4 142 TYR 0.008 0.002 TYR10 184 ARG 0.001 0.000 ARG11 179 *********************** 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 23 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 11 210 ILE cc_start: 0.7929 (mp) cc_final: 0.7255 (mp) REVERT: 11 223 ASP cc_start: 0.5892 (t0) cc_final: 0.5672 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1658 time to fit residues: 4.1307 Evaluate side-chains 19 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 53 optimal weight: 0.0060 overall best weight: 2.6600 ------------------------------------------------------------------------------- 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: 0.7044 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9888 Z= 0.230 Angle : 0.677 4.045 13260 Z= 0.361 Chirality : 0.051 0.176 1476 Planarity : 0.005 0.042 1704 Dihedral : 6.384 23.019 1260 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 27.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -3.74 (0.22), residues: 1188 helix: None (None), residues: 0 sheet: -1.09 (0.23), residues: 456 loop : -3.65 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 1 129 HIS 0.000 0.000 HIS 1 136 PHE 0.012 0.003 PHE 4 142 TYR 0.002 0.001 TYR 9 184 ARG 0.003 0.001 ARG 6 141 *********************** 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 23 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.125 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1613 time to fit residues: 4.0607 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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: 8.9990 chunk 46 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 0.0060 chunk 57 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9888 Z= 0.232 Angle : 0.717 6.575 13260 Z= 0.381 Chirality : 0.055 0.193 1476 Planarity : 0.005 0.046 1704 Dihedral : 6.297 20.478 1260 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 1.06 % Allowed : 1.06 % 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: -4.18 (0.20), residues: 1188 helix: None (None), residues: 0 sheet: -1.60 (0.21), residues: 456 loop : -3.81 (0.18), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 1 129 HIS 0.000 0.000 HIS 1 136 PHE 0.014 0.003 PHE 5 142 TYR 0.001 0.001 TYR 9 184 ARG 0.003 0.001 ARG10 219 *********************** 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 21 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: 11 136 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.7244 (t-90) REVERT: 11 210 ILE cc_start: 0.7823 (mp) cc_final: 0.7550 (mp) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0936 time to fit residues: 2.2654 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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: 9.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.0470 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 97 optimal weight: 0.0970 chunk 70 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9888 Z= 0.203 Angle : 0.775 7.478 13260 Z= 0.399 Chirality : 0.055 0.186 1476 Planarity : 0.005 0.046 1704 Dihedral : 5.849 17.129 1260 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % 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: -3.65 (0.20), residues: 1188 helix: None (None), residues: 0 sheet: -1.22 (0.19), residues: 492 loop : -3.52 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP11 176 HIS 0.009 0.006 HIS10 136 PHE 0.011 0.003 PHE11 209 TYR 0.005 0.001 TYR 4 184 ARG 0.002 0.001 ARG 1 219 *********************** 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 18 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: 11 203 LEU cc_start: 0.7900 (tp) cc_final: 0.6963 (pt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0661 time to fit residues: 1.4597 Evaluate side-chains 13 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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: 4.9990 chunk 79 optimal weight: 0.0670 chunk 119 optimal weight: 0.0000 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.4272 ------------------------------------------------------------------------------- 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: 0.6818 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9888 Z= 0.214 Angle : 0.792 6.411 13260 Z= 0.408 Chirality : 0.057 0.245 1476 Planarity : 0.005 0.045 1704 Dihedral : 5.843 19.407 1260 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % 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: -3.42 (0.20), residues: 1188 helix: None (None), residues: 0 sheet: -0.65 (0.20), residues: 432 loop : -3.52 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 9 129 HIS 0.002 0.001 HIS 7 136 PHE 0.016 0.003 PHE 6 209 TYR 0.008 0.002 TYR 4 184 ARG 0.001 0.000 ARG11 179 ********************** 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 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 REVERT: 11 218 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5708 (mm-30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1010 time to fit residues: 2.1210 Evaluate side-chains 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 0.0870 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.041143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.031391 restraints weight = 9771.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.031995 restraints weight = 7528.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.032468 restraints weight = 6339.656| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.8102 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= 0.213 Angle : 0.746 5.258 13260 Z= 0.387 Chirality : 0.052 0.154 1476 Planarity : 0.005 0.045 1704 Dihedral : 5.919 19.565 1260 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % 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: -3.70 (0.20), residues: 1188 helix: None (None), residues: 0 sheet: -1.52 (0.18), residues: 516 loop : -3.38 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP11 176 HIS 0.002 0.001 HIS10 136 PHE 0.012 0.002 PHE 6 209 TYR 0.007 0.002 TYR 4 184 ARG 0.001 0.001 ARG11 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.23 seconds wall clock time: 34 minutes 14.05 seconds (2054.05 seconds total)