Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 22:59:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/08_2023/7u6v_26381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/08_2023/7u6v_26381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/08_2023/7u6v_26381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/08_2023/7u6v_26381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/08_2023/7u6v_26381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/08_2023/7u6v_26381.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5073 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 23 5.16 5 C 3168 2.51 5 N 854 2.21 5 O 1051 1.98 5 H 4901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 10": Residue "C PHE 10": Residue "C ASP 17": "OD1" <-> "OD2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 9997 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4485 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 4416 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 282, 4416 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 bond proxies already assigned to first conformer: 4386 Chain: "B" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1058 Chain: "C" Number of atoms: 1105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1066 Classifications: {'peptide': 70} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1035 Chain: "D" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1054 Classifications: {'peptide': 69} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Chain: "E" Number of atoms: 1079 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1064 Chain: "F" Number of atoms: 1083 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 1067 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 70, 1068 Classifications: {'peptide': 70} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} bond proxies already assigned to first conformer: 1061 Chain: "P" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASER A 99 " occ=0.38 ... (20 atoms not shown) pdb=" HG BSER A 99 " occ=0.62 residue: pdb=" N AARG A 119 " occ=0.59 ... (46 atoms not shown) pdb="HH22BARG A 119 " occ=0.41 residue: pdb=" N ASER A 278 " occ=0.27 ... (20 atoms not shown) pdb=" HG BSER A 278 " occ=0.73 residue: pdb=" N AVAL B 65 " occ=0.74 ... (30 atoms not shown) pdb="HG23BVAL B 65 " occ=0.26 residue: pdb=" N AGLU C 9 " occ=0.47 ... (28 atoms not shown) pdb=" HG3BGLU C 9 " occ=0.53 residue: pdb=" N ASER C 60 " occ=0.61 ... (20 atoms not shown) pdb=" HG BSER C 60 " occ=0.39 residue: pdb=" N ASER E 60 " occ=0.38 ... (20 atoms not shown) pdb=" HG BSER E 60 " occ=0.62 residue: pdb=" N ACYS F 3 " occ=0.68 ... (19 atoms not shown) pdb=" HG BCYS F 3 " occ=0.32 Time building chain proxies: 7.92, per 1000 atoms: 0.79 Number of scatterers: 9997 At special positions: 0 Unit cell: (78.356, 97.3264, 109.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 O 1051 8.00 N 854 7.00 C 3168 6.00 H 4901 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 56 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 56 " distance=2.03 Simple disulfide: pdb=" SG ACYS F 3 " - pdb=" SG CYS F 56 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 28.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 151 through 164 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.366A pdb=" N GLN A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.042A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 removed outlier: 4.079A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.600A pdb=" N TYR A 293 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.940A pdb=" N LEU B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 45 removed outlier: 4.522A pdb=" N LEU C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.695A pdb=" N LEU D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 45 Processing helix chain 'F' and resid 34 through 46 removed outlier: 4.578A pdb=" N LEU F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN F 40 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 5.105A pdb=" N LEU A 67 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 72 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 78 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.570A pdb=" N TYR A 189 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 225 removed outlier: 6.849A pdb=" N GLY A 217 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLU A 277 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ARG A 219 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 6 removed outlier: 6.485A pdb=" N ILE B 51 " --> pdb=" O CYS B 3 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 49 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.944A pdb=" N PHE C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU C 64 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.667A pdb=" N GLU D 64 " --> pdb=" O LYS D 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.742A pdb=" N THR D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.614A pdb=" N PHE E 10 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 23 " --> pdb=" O LYS E 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 6 removed outlier: 4.213A pdb=" N ALA F 4 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.439A pdb=" N PHE F 10 " --> pdb=" O LYS F 22 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 575 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: 3.80 Time building geometry restraints manager: 8.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4900 1.03 - 1.23: 25 1.23 - 1.43: 2212 1.43 - 1.62: 2904 1.62 - 1.82: 33 Bond restraints: 10074 Sorted by residual: bond pdb=" C SER A 37 " pdb=" N VAL A 38 " ideal model delta sigma weight residual 1.335 1.325 0.010 1.41e-02 5.03e+03 5.00e-01 bond pdb=" N THR C 20 " pdb=" CA THR C 20 " ideal model delta sigma weight residual 1.463 1.454 0.009 1.28e-02 6.10e+03 4.60e-01 bond pdb=" CA VAL C 21 " pdb=" C VAL C 21 " ideal model delta sigma weight residual 1.526 1.520 0.006 1.04e-02 9.25e+03 3.69e-01 bond pdb=" CA VAL A 38 " pdb=" CB VAL A 38 " ideal model delta sigma weight residual 1.538 1.544 -0.007 1.10e-02 8.26e+03 3.50e-01 bond pdb=" CA GLU C 64 " pdb=" C GLU C 64 " ideal model delta sigma weight residual 1.529 1.523 0.006 1.04e-02 9.25e+03 3.43e-01 ... (remaining 10069 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.67: 50 105.67 - 112.75: 11412 112.75 - 119.83: 2660 119.83 - 126.91: 3909 126.91 - 133.99: 53 Bond angle restraints: 18084 Sorted by residual: angle pdb=" CB ARG A 156 " pdb=" CG ARG A 156 " pdb=" CD ARG A 156 " ideal model delta sigma weight residual 111.30 117.77 -6.47 2.30e+00 1.89e-01 7.91e+00 angle pdb=" CB ARG A 21 " pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " ideal model delta sigma weight residual 111.30 117.34 -6.04 2.30e+00 1.89e-01 6.89e+00 angle pdb=" N VAL C 21 " pdb=" CA VAL C 21 " pdb=" C VAL C 21 " ideal model delta sigma weight residual 110.05 107.66 2.39 1.09e+00 8.42e-01 4.79e+00 angle pdb=" N VAL A 38 " pdb=" CA VAL A 38 " pdb=" C VAL A 38 " ideal model delta sigma weight residual 110.21 107.80 2.41 1.13e+00 7.83e-01 4.56e+00 angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta sigma weight residual 110.12 113.12 -3.00 1.47e+00 4.63e-01 4.15e+00 ... (remaining 18079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3757 17.97 - 35.94: 286 35.94 - 53.91: 47 53.91 - 71.88: 9 71.88 - 89.85: 5 Dihedral angle restraints: 4104 sinusoidal: 1879 harmonic: 2225 Sorted by residual: dihedral pdb=" CB CYS E 3 " pdb=" SG CYS E 3 " pdb=" SG CYS E 56 " pdb=" CB CYS E 56 " ideal model delta sinusoidal sigma weight residual -86.00 -56.34 -29.66 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 56 " pdb=" CB CYS C 56 " ideal model delta sinusoidal sigma weight residual -86.00 -57.64 -28.36 1 1.00e+01 1.00e-02 1.15e+01 dihedral pdb=" CA CYS D 3 " pdb=" CB CYS D 3 " pdb=" SG CYS D 3 " pdb=" SG CYS D 56 " ideal model delta sinusoidal sigma weight residual 79.00 22.66 56.34 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 482 0.028 - 0.056: 202 0.056 - 0.085: 41 0.085 - 0.113: 48 0.113 - 0.141: 14 Chirality restraints: 787 Sorted by residual: chirality pdb=" CA VAL C 65 " pdb=" N VAL C 65 " pdb=" C VAL C 65 " pdb=" CB VAL C 65 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 784 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 209 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 210 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.010 9.50e-02 1.11e+02 6.87e-03 8.19e-01 pdb=" NE ARG A 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " 0.003 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 36 " -0.005 2.00e-02 2.50e+03 8.94e-03 7.99e-01 pdb=" C GLN E 36 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN E 36 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO E 37 " -0.005 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 562 2.15 - 2.76: 20224 2.76 - 3.37: 29497 3.37 - 3.99: 37774 3.99 - 4.60: 57473 Nonbonded interactions: 145530 Sorted by model distance: nonbonded pdb=" OE2 GLU A 72 " pdb=" H TYR A 77 " model vdw 1.531 1.850 nonbonded pdb=" H HIS A 66 " pdb=" OH TYR A 139 " model vdw 1.550 1.850 nonbonded pdb=" OD1 ASP E 16 " pdb=" HG1 THR E 18 " model vdw 1.572 1.850 nonbonded pdb=" O ILE A 54 " pdb="HH11 ARG A 55 " model vdw 1.584 1.850 nonbonded pdb=" OD1 ASN C 14 " pdb=" H GLU C 15 " model vdw 1.591 1.850 ... (remaining 145525 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 'B' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 70)) selection = (chain 'C' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 70)) selection = (chain 'D' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 59 or resid 62 t \ hrough 64 or resid 67 through 70)) selection = (chain 'E' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \ name HB2 or name HB3)))) selection = (chain 'F' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \ resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \ through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \ name HB2 or name HB3)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.12 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.190 Extract box with map and model: 6.240 Check model and map are aligned: 0.180 Set scattering table: 0.090 Process input model: 39.380 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3344 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 : 0.002 0.016 5173 Z= 0.146 Angle : 0.524 6.467 7012 Z= 0.315 Chirality : 0.041 0.141 787 Planarity : 0.002 0.037 908 Dihedral : 13.786 88.086 1861 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.34), residues: 643 helix: 1.06 (0.47), residues: 159 sheet: -0.12 (0.42), residues: 150 loop : -0.62 (0.33), residues: 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3518 time to fit residues: 45.5945 Evaluate side-chains 84 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.0000 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3422 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5173 Z= 0.167 Angle : 0.487 4.508 7012 Z= 0.272 Chirality : 0.041 0.137 787 Planarity : 0.003 0.032 908 Dihedral : 4.324 52.371 695 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.34), residues: 643 helix: 0.84 (0.45), residues: 164 sheet: -0.08 (0.44), residues: 136 loop : -0.68 (0.33), residues: 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.3438 time to fit residues: 47.1139 Evaluate side-chains 87 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1664 time to fit residues: 1.1394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3417 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 5173 Z= 0.157 Angle : 0.477 4.540 7012 Z= 0.266 Chirality : 0.041 0.132 787 Planarity : 0.003 0.032 908 Dihedral : 4.348 52.855 695 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.33), residues: 643 helix: 0.51 (0.44), residues: 164 sheet: -0.21 (0.44), residues: 132 loop : -0.78 (0.33), residues: 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3459 time to fit residues: 46.6266 Evaluate side-chains 87 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3465 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5173 Z= 0.170 Angle : 0.490 5.636 7012 Z= 0.274 Chirality : 0.041 0.166 787 Planarity : 0.003 0.033 908 Dihedral : 4.408 52.276 695 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.33), residues: 643 helix: 0.54 (0.44), residues: 164 sheet: -0.37 (0.42), residues: 136 loop : -0.81 (0.33), residues: 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3128 time to fit residues: 43.0213 Evaluate side-chains 87 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3467 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5173 Z= 0.164 Angle : 0.487 4.560 7012 Z= 0.272 Chirality : 0.041 0.147 787 Planarity : 0.003 0.027 908 Dihedral : 4.408 52.555 695 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.32), residues: 643 helix: 0.47 (0.44), residues: 159 sheet: -0.42 (0.42), residues: 137 loop : -0.93 (0.32), residues: 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3183 time to fit residues: 42.7867 Evaluate side-chains 86 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3460 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 5173 Z= 0.159 Angle : 0.488 6.011 7012 Z= 0.271 Chirality : 0.041 0.141 787 Planarity : 0.003 0.039 908 Dihedral : 4.400 52.904 695 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.33), residues: 643 helix: 0.50 (0.45), residues: 160 sheet: -0.31 (0.43), residues: 132 loop : -0.93 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3453 time to fit residues: 47.4777 Evaluate side-chains 90 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3452 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5173 Z= 0.156 Angle : 0.491 6.916 7012 Z= 0.271 Chirality : 0.041 0.145 787 Planarity : 0.003 0.028 908 Dihedral : 4.406 53.134 695 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.33), residues: 643 helix: 0.48 (0.45), residues: 159 sheet: -0.36 (0.43), residues: 137 loop : -0.91 (0.32), residues: 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3139 time to fit residues: 42.5283 Evaluate side-chains 86 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3438 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 5173 Z= 0.150 Angle : 0.475 5.838 7012 Z= 0.265 Chirality : 0.041 0.143 787 Planarity : 0.003 0.029 908 Dihedral : 4.405 53.384 695 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.33), residues: 643 helix: 0.53 (0.45), residues: 160 sheet: -0.35 (0.42), residues: 137 loop : -0.88 (0.32), residues: 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3273 time to fit residues: 45.0776 Evaluate side-chains 88 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3443 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5173 Z= 0.151 Angle : 0.479 5.797 7012 Z= 0.268 Chirality : 0.041 0.143 787 Planarity : 0.003 0.027 908 Dihedral : 4.402 53.178 695 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.33), residues: 643 helix: 0.59 (0.45), residues: 160 sheet: -0.25 (0.43), residues: 132 loop : -0.92 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3142 time to fit residues: 42.4049 Evaluate side-chains 87 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3414 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 5173 Z= 0.144 Angle : 0.486 6.155 7012 Z= 0.267 Chirality : 0.041 0.154 787 Planarity : 0.003 0.028 908 Dihedral : 4.395 53.756 695 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.33), residues: 643 helix: 0.62 (0.45), residues: 160 sheet: -0.17 (0.43), residues: 132 loop : -0.89 (0.32), residues: 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3118 time to fit residues: 42.8303 Evaluate side-chains 87 residues out of total 537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.094931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058806 restraints weight = 211748.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.066353 restraints weight = 88612.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.072406 restraints weight = 50610.439| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5173 Z= 0.135 Angle : 0.474 5.536 7012 Z= 0.262 Chirality : 0.041 0.146 787 Planarity : 0.003 0.029 908 Dihedral : 4.360 54.360 695 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.33), residues: 643 helix: 0.52 (0.45), residues: 161 sheet: -0.21 (0.43), residues: 137 loop : -0.80 (0.33), residues: 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.37 seconds wall clock time: 60 minutes 13.44 seconds (3613.44 seconds total)