Starting phenix.real_space_refine on Thu Jun 12 10:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u6v_26381/06_2025/7u6v_26381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u6v_26381/06_2025/7u6v_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/cci-nas-00/data/ceres_data/7u6v_26381/06_2025/7u6v_26381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u6v_26381/06_2025/7u6v_26381.map" model { file = "/net/cci-nas-00/data/ceres_data/7u6v_26381/06_2025/7u6v_26381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u6v_26381/06_2025/7u6v_26381.cif" } 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. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.35, per 1000 atoms: 0.94 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 - 3.00 Amino acid : True - 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 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: 0.98 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: 3.46 Time building geometry restraints manager: 3.05 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: 0.00 - 1.29: 17557 1.29 - 2.59: 499 2.59 - 3.88: 23 3.88 - 5.17: 3 5.17 - 6.47: 2 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: 4365 17.97 - 35.94: 329 35.94 - 53.91: 73 53.91 - 71.88: 20 71.88 - 89.85: 5 Dihedral angle restraints: 4792 sinusoidal: 2567 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 4789 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 2.450 nonbonded pdb=" H HIS A 66 " pdb=" OH TYR A 139 " model vdw 1.550 2.450 nonbonded pdb=" OD1 ASP E 16 " pdb=" HG1 THR E 18 " model vdw 1.572 2.450 nonbonded pdb=" O ILE A 54 " pdb="HH11 ARG A 55 " model vdw 1.584 2.450 nonbonded pdb=" OD1 ASN C 14 " pdb=" H GLU C 15 " model vdw 1.591 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.210 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.000 Find NCS groups from input model: 0.240 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- 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 5179 Z= 0.124 Angle : 0.525 6.467 7024 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 % Allowed : 0.52 % Favored : 97.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 33 HIS 0.004 0.001 HIS A 66 PHE 0.009 0.001 PHE A 81 TYR 0.013 0.001 TYR A 139 ARG 0.013 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.18667 ( 214) hydrogen bonds : angle 6.85698 ( 575) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.78644 ( 12) covalent geometry : bond 0.00227 ( 5173) covalent geometry : angle 0.52429 ( 7012) *********************** 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 to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.778 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: A 108 MET cc_start: 0.0664 (tpp) cc_final: 0.0400 (tpp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3375 time to fit residues: 43.6677 Evaluate side-chains 84 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN C 43 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.092936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.058871 restraints weight = 200921.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.066054 restraints weight = 87898.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.071933 restraints weight = 51300.657| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5179 Z= 0.190 Angle : 0.574 5.021 7024 Z= 0.322 Chirality : 0.042 0.138 787 Planarity : 0.005 0.042 908 Dihedral : 4.714 56.709 695 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.75 % Allowed : 3.85 % Favored : 94.41 % 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: -0.75 (0.32), residues: 643 helix: 0.63 (0.45), residues: 163 sheet: -0.29 (0.44), residues: 131 loop : -1.13 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 33 HIS 0.004 0.001 HIS A 66 PHE 0.014 0.002 PHE E 19 TYR 0.013 0.002 TYR B 13 ARG 0.010 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 214) hydrogen bonds : angle 6.14406 ( 575) SS BOND : bond 0.00353 ( 6) SS BOND : angle 1.26041 ( 12) covalent geometry : bond 0.00389 ( 5173) covalent geometry : angle 0.57222 ( 7012) *********************** 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 107 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.838 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: F 12 LYS cc_start: 0.7790 (tptt) cc_final: 0.7499 (tptt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3539 time to fit residues: 49.4198 Evaluate side-chains 90 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.094230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.059966 restraints weight = 211763.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.067592 restraints weight = 89883.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.073600 restraints weight = 51380.478| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5179 Z= 0.151 Angle : 0.534 4.455 7024 Z= 0.298 Chirality : 0.042 0.139 787 Planarity : 0.004 0.065 908 Dihedral : 4.713 57.958 695 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.75 % Allowed : 3.50 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.31), residues: 643 helix: 0.15 (0.43), residues: 164 sheet: -0.50 (0.43), residues: 131 loop : -1.19 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 29 HIS 0.004 0.001 HIS A 66 PHE 0.019 0.002 PHE E 62 TYR 0.012 0.002 TYR B 13 ARG 0.006 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 214) hydrogen bonds : angle 6.06186 ( 575) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.14099 ( 12) covalent geometry : bond 0.00309 ( 5173) covalent geometry : angle 0.53240 ( 7012) *********************** 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 106 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.690 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: F 47 MET cc_start: 0.6131 (mmm) cc_final: 0.5789 (mmt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3500 time to fit residues: 48.8358 Evaluate side-chains 90 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 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 = 0.4010 r_free = 0.4010 target = 0.093752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.060122 restraints weight = 204956.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.067681 restraints weight = 88906.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.073687 restraints weight = 51377.527| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5179 Z= 0.143 Angle : 0.536 5.795 7024 Z= 0.299 Chirality : 0.042 0.151 787 Planarity : 0.004 0.044 908 Dihedral : 4.749 59.048 695 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.75 % Allowed : 2.80 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.31), residues: 643 helix: 0.10 (0.42), residues: 168 sheet: -0.56 (0.43), residues: 131 loop : -1.21 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 29 HIS 0.003 0.001 HIS A 66 PHE 0.018 0.002 PHE E 62 TYR 0.012 0.002 TYR C 28 ARG 0.016 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 214) hydrogen bonds : angle 5.97069 ( 575) SS BOND : bond 0.00311 ( 6) SS BOND : angle 1.15514 ( 12) covalent geometry : bond 0.00297 ( 5173) covalent geometry : angle 0.53411 ( 7012) *********************** 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 107 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.711 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: 107 average time/residue: 0.3413 time to fit residues: 47.7590 Evaluate side-chains 90 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 11 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.0000 chunk 57 optimal weight: 0.0870 overall best weight: 0.2480 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.096892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.062453 restraints weight = 221374.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.070425 restraints weight = 92606.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.076694 restraints weight = 52498.836| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5179 Z= 0.109 Angle : 0.509 4.548 7024 Z= 0.283 Chirality : 0.042 0.140 787 Planarity : 0.004 0.040 908 Dihedral : 4.616 61.377 695 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.57 % Allowed : 1.40 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.32), residues: 643 helix: 0.17 (0.42), residues: 163 sheet: -0.44 (0.44), residues: 129 loop : -1.08 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 33 HIS 0.003 0.001 HIS A 66 PHE 0.012 0.001 PHE E 62 TYR 0.013 0.001 TYR A 293 ARG 0.016 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 214) hydrogen bonds : angle 5.78548 ( 575) SS BOND : bond 0.00287 ( 6) SS BOND : angle 1.10200 ( 12) covalent geometry : bond 0.00235 ( 5173) covalent geometry : angle 0.50719 ( 7012) *********************** 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 113 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.824 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: F 47 MET cc_start: 0.5982 (mmm) cc_final: 0.5599 (mmt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.3366 time to fit residues: 50.0185 Evaluate side-chains 94 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 66 GLN ** 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 = 0.4056 r_free = 0.4056 target = 0.096718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.062769 restraints weight = 188975.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.070714 restraints weight = 81895.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.076849 restraints weight = 46468.909| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5179 Z= 0.104 Angle : 0.509 6.732 7024 Z= 0.281 Chirality : 0.042 0.141 787 Planarity : 0.003 0.035 908 Dihedral : 4.537 61.888 695 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.57 % Allowed : 1.75 % Favored : 96.68 % 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: -0.80 (0.32), residues: 643 helix: 0.19 (0.42), residues: 164 sheet: -0.36 (0.44), residues: 131 loop : -0.91 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 29 HIS 0.005 0.001 HIS A 66 PHE 0.012 0.001 PHE E 62 TYR 0.027 0.001 TYR A 139 ARG 0.013 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 214) hydrogen bonds : angle 5.68147 ( 575) SS BOND : bond 0.00271 ( 6) SS BOND : angle 1.02510 ( 12) covalent geometry : bond 0.00226 ( 5173) covalent geometry : angle 0.50761 ( 7012) *********************** 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 114 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.711 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: A 6 ASP cc_start: 0.9040 (t0) cc_final: 0.8726 (t70) REVERT: F 47 MET cc_start: 0.5992 (mmm) cc_final: 0.5547 (mmt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3209 time to fit residues: 47.9620 Evaluate side-chains 97 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.094060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059693 restraints weight = 207733.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.067418 restraints weight = 90671.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.073585 restraints weight = 52158.113| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5179 Z= 0.136 Angle : 0.523 6.400 7024 Z= 0.293 Chirality : 0.042 0.157 787 Planarity : 0.004 0.047 908 Dihedral : 4.602 59.268 695 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.57 % Allowed : 1.57 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.32), residues: 643 helix: 0.11 (0.42), residues: 168 sheet: -0.46 (0.43), residues: 131 loop : -0.97 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 29 HIS 0.003 0.001 HIS A 66 PHE 0.014 0.001 PHE E 62 TYR 0.012 0.002 TYR C 28 ARG 0.010 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 214) hydrogen bonds : angle 5.81629 ( 575) SS BOND : bond 0.00283 ( 6) SS BOND : angle 1.04930 ( 12) covalent geometry : bond 0.00283 ( 5173) covalent geometry : angle 0.52200 ( 7012) *********************** 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 109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.730 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: A 6 ASP cc_start: 0.9094 (t0) cc_final: 0.8800 (t70) REVERT: A 272 ASN cc_start: 0.8308 (m-40) cc_final: 0.8009 (m110) REVERT: F 47 MET cc_start: 0.6195 (mmm) cc_final: 0.5705 (mmt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3434 time to fit residues: 49.1377 Evaluate side-chains 96 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.0770 chunk 41 optimal weight: 0.0870 chunk 47 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.096228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.064020 restraints weight = 165106.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.071477 restraints weight = 78168.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.077309 restraints weight = 45914.626| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5179 Z= 0.105 Angle : 0.510 6.068 7024 Z= 0.282 Chirality : 0.042 0.148 787 Planarity : 0.003 0.031 908 Dihedral : 4.562 60.645 695 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.57 % Allowed : 1.22 % Favored : 97.20 % 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: -0.80 (0.32), residues: 643 helix: 0.34 (0.43), residues: 163 sheet: -0.38 (0.44), residues: 130 loop : -0.98 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 29 HIS 0.004 0.001 HIS A 66 PHE 0.026 0.001 PHE C 19 TYR 0.010 0.001 TYR A 139 ARG 0.012 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 214) hydrogen bonds : angle 5.68754 ( 575) SS BOND : bond 0.00264 ( 6) SS BOND : angle 1.02297 ( 12) covalent geometry : bond 0.00233 ( 5173) covalent geometry : angle 0.50864 ( 7012) *********************** 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 114 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.782 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: A 6 ASP cc_start: 0.9091 (t0) cc_final: 0.8791 (t70) REVERT: A 272 ASN cc_start: 0.8171 (m-40) cc_final: 0.7871 (m110) REVERT: F 47 MET cc_start: 0.6082 (mmm) cc_final: 0.5598 (mmt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3252 time to fit residues: 48.7664 Evaluate side-chains 95 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.095165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060678 restraints weight = 202059.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.068506 restraints weight = 87096.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.074470 restraints weight = 49792.125| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-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: 84 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5179 Z= 0.114 Angle : 0.516 5.995 7024 Z= 0.286 Chirality : 0.041 0.144 787 Planarity : 0.003 0.033 908 Dihedral : 4.583 60.025 695 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.57 % Allowed : 1.05 % Favored : 97.38 % 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: -0.81 (0.32), residues: 643 helix: 0.35 (0.43), residues: 163 sheet: -0.42 (0.44), residues: 130 loop : -0.98 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 276 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.001 PHE E 62 TYR 0.010 0.001 TYR C 28 ARG 0.011 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 214) hydrogen bonds : angle 5.62143 ( 575) SS BOND : bond 0.00271 ( 6) SS BOND : angle 1.01747 ( 12) covalent geometry : bond 0.00247 ( 5173) covalent geometry : angle 0.51467 ( 7012) *********************** 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 109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.120 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: A 6 ASP cc_start: 0.9099 (t0) cc_final: 0.8810 (t70) REVERT: A 272 ASN cc_start: 0.7675 (m-40) cc_final: 0.7358 (m110) REVERT: E 57 GLU cc_start: 0.8465 (mp0) cc_final: 0.8206 (mp0) REVERT: F 47 MET cc_start: 0.6160 (mmm) cc_final: 0.5609 (mmt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3822 time to fit residues: 55.4168 Evaluate side-chains 92 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.095917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.061194 restraints weight = 194459.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.069102 restraints weight = 82976.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.075078 restraints weight = 47353.666| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5179 Z= 0.111 Angle : 0.536 8.811 7024 Z= 0.294 Chirality : 0.042 0.141 787 Planarity : 0.003 0.044 908 Dihedral : 4.577 60.361 695 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.57 % Allowed : 0.87 % Favored : 97.55 % 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: -0.83 (0.32), residues: 643 helix: 0.25 (0.42), residues: 164 sheet: -0.40 (0.44), residues: 130 loop : -0.96 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 276 HIS 0.004 0.001 HIS A 66 PHE 0.014 0.001 PHE A 7 TYR 0.026 0.002 TYR A 139 ARG 0.017 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 214) hydrogen bonds : angle 5.60685 ( 575) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.00941 ( 12) covalent geometry : bond 0.00245 ( 5173) covalent geometry : angle 0.53478 ( 7012) ********************** 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 111 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.867 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: A 272 ASN cc_start: 0.7656 (m-40) cc_final: 0.7271 (m110) REVERT: E 57 GLU cc_start: 0.8411 (mp0) cc_final: 0.8155 (mp0) REVERT: F 47 MET cc_start: 0.6212 (mmm) cc_final: 0.5651 (mmt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.4327 time to fit residues: 63.1745 Evaluate side-chains 95 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.095741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.061013 restraints weight = 182413.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068745 restraints weight = 78930.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.074727 restraints weight = 45404.765| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5179 Z= 0.104 Angle : 0.518 7.301 7024 Z= 0.285 Chirality : 0.042 0.142 787 Planarity : 0.003 0.035 908 Dihedral : 4.523 60.628 695 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.57 % Allowed : 0.87 % Favored : 97.55 % 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: -0.75 (0.33), residues: 643 helix: 0.29 (0.42), residues: 168 sheet: -0.35 (0.45), residues: 130 loop : -0.91 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 276 HIS 0.004 0.001 HIS A 66 PHE 0.011 0.001 PHE E 62 TYR 0.013 0.001 TYR A 139 ARG 0.013 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 214) hydrogen bonds : angle 5.55487 ( 575) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.99969 ( 12) covalent geometry : bond 0.00229 ( 5173) covalent geometry : angle 0.51667 ( 7012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6236.52 seconds wall clock time: 109 minutes 23.28 seconds (6563.28 seconds total)