Starting phenix.real_space_refine on Wed Mar 12 08:46:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cx0_27032/03_2025/8cx0_27032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx0_27032/03_2025/8cx0_27032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cx0_27032/03_2025/8cx0_27032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx0_27032/03_2025/8cx0_27032.map" model { file = "/net/cci-nas-00/data/ceres_data/8cx0_27032/03_2025/8cx0_27032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx0_27032/03_2025/8cx0_27032.cif" } resolution = 2.7 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= -0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 8 5.49 5 S 47 5.16 5 C 4798 2.51 5 N 1346 2.21 5 O 1373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7575 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3200 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "C" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1276 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain breaks: 1 Chain: "K" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 4} Link IDs: {'rna2p': 3, 'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 288 20.523 21.995 37.524 1.00 61.84 S ATOM 2469 SG CYS A 291 21.392 24.957 38.126 1.00 56.62 S ATOM 813 SG CYS A 97 41.384 56.405 50.521 1.00 39.00 S ATOM 835 SG CYS A 100 44.558 55.360 52.399 1.00 42.31 S ATOM 4184 SG CYS B 114 18.078 86.830 54.083 1.00 63.17 S ATOM 4328 SG CYS B 133 21.300 85.170 55.518 1.00 67.06 S Time building chain proxies: 5.03, per 1000 atoms: 0.66 Number of scatterers: 7575 At special positions: 0 Unit cell: (80.16, 141.115, 86.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 47 16.00 P 8 15.00 O 1373 8.00 N 1346 7.00 C 4798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.67 Conformation dependent library (CDL) restraints added in 900.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 257 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 288 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 291 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 65 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 100 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 139 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 108 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 133 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 114 " Number of angles added : 2 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 40.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.522A pdb=" N LYS A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 153 through 165 removed outlier: 3.840A pdb=" N VAL A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 267 through 270 removed outlier: 3.513A pdb=" N LYS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.844A pdb=" N GLU A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.546A pdb=" N VAL A 351 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'B' and resid 14 through 31 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.526A pdb=" N GLY B 138 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'C' and resid 6 through 15 Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 129 through 135 removed outlier: 4.636A pdb=" N GLN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 removed outlier: 3.729A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.702A pdb=" N GLY D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 removed outlier: 3.528A pdb=" N GLU D 41 " --> pdb=" O PRO D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'E' and resid 32 through 38 removed outlier: 3.638A pdb=" N THR E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 96 through 111 removed outlier: 4.366A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.638A pdb=" N ASP A 50 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TRP A 34 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TRP A 94 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N THR A 148 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 116 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LYS A 150 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 118 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 243 removed outlier: 5.048A pdb=" N VAL A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN A 237 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N TYR A 222 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N ARG A 239 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N LEU A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.496A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 83 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE B 87 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 9 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N TRP B 89 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N VAL B 7 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 18.510A pdb=" N LYS B 91 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 21.069A pdb=" N TRP B 5 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 64 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 120 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.496A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N SER B 95 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE C 102 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.552A pdb=" N ILE D 14 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 7 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 16 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE D 4 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL D 75 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET D 6 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.156A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 969 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: 1.91 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1269 1.32 - 1.44: 2297 1.44 - 1.57: 4153 1.57 - 1.69: 15 1.69 - 1.81: 68 Bond restraints: 7802 Sorted by residual: bond pdb=" CA ASP A 130 " pdb=" C ASP A 130 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.29e-02 6.01e+03 1.86e+01 bond pdb=" N ASP A 130 " pdb=" CA ASP A 130 " ideal model delta sigma weight residual 1.459 1.417 0.042 1.23e-02 6.61e+03 1.18e+01 bond pdb=" N THR B 20 " pdb=" CA THR B 20 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.23e-02 6.61e+03 9.58e+00 bond pdb=" N ASP A 264 " pdb=" CA ASP A 264 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.23e-02 6.61e+03 9.48e+00 bond pdb=" C THR B 20 " pdb=" O THR B 20 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.19e-02 7.06e+03 9.41e+00 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 10369 2.12 - 4.24: 186 4.24 - 6.37: 24 6.37 - 8.49: 8 8.49 - 10.61: 1 Bond angle restraints: 10588 Sorted by residual: angle pdb=" N GLU C 152 " pdb=" CA GLU C 152 " pdb=" C GLU C 152 " ideal model delta sigma weight residual 110.24 120.85 -10.61 1.41e+00 5.03e-01 5.66e+01 angle pdb=" N TRP A 77 " pdb=" CA TRP A 77 " pdb=" C TRP A 77 " ideal model delta sigma weight residual 111.82 103.74 8.08 1.16e+00 7.43e-01 4.85e+01 angle pdb=" N GLY C 31 " pdb=" CA GLY C 31 " pdb=" C GLY C 31 " ideal model delta sigma weight residual 111.36 119.40 -8.04 1.17e+00 7.31e-01 4.72e+01 angle pdb=" N ASP C 34 " pdb=" CA ASP C 34 " pdb=" C ASP C 34 " ideal model delta sigma weight residual 111.33 119.34 -8.01 1.21e+00 6.83e-01 4.38e+01 angle pdb=" N GLY A 255 " pdb=" CA GLY A 255 " pdb=" C GLY A 255 " ideal model delta sigma weight residual 111.93 119.48 -7.55 1.15e+00 7.56e-01 4.31e+01 ... (remaining 10583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4159 17.45 - 34.89: 362 34.89 - 52.34: 71 52.34 - 69.78: 12 69.78 - 87.23: 13 Dihedral angle restraints: 4617 sinusoidal: 2005 harmonic: 2612 Sorted by residual: dihedral pdb=" CA PHE C 17 " pdb=" C PHE C 17 " pdb=" N PHE C 18 " pdb=" CA PHE C 18 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N PHE C 17 " pdb=" CA PHE C 17 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA TYR B 110 " pdb=" C TYR B 110 " pdb=" N TYR B 111 " pdb=" CA TYR B 111 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 4614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 931 0.059 - 0.118: 133 0.118 - 0.177: 27 0.177 - 0.236: 4 0.236 - 0.295: 1 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA HIS A 81 " pdb=" N HIS A 81 " pdb=" C HIS A 81 " pdb=" CB HIS A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ARG A 29 " pdb=" N ARG A 29 " pdb=" C ARG A 29 " pdb=" CB ARG A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' A K 3 " pdb=" C4' A K 3 " pdb=" O3' A K 3 " pdb=" C2' A K 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1093 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 82 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY B 82 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY B 82 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN B 83 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 73 " -0.012 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C HIS B 73 " 0.045 2.00e-02 2.50e+03 pdb=" O HIS B 73 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 65 " 0.032 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO E 66 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " 0.027 5.00e-02 4.00e+02 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1812 2.80 - 3.32: 6846 3.32 - 3.85: 12243 3.85 - 4.37: 14869 4.37 - 4.90: 24860 Nonbonded interactions: 60630 Sorted by model distance: nonbonded pdb=" NH2 ARG D 37 " pdb=" O ARG D 80 " model vdw 2.270 3.120 nonbonded pdb=" N GLU E 12 " pdb=" OE1 GLU E 12 " model vdw 2.278 3.120 nonbonded pdb=" O ARG D 9 " pdb=" OG1 THR D 12 " model vdw 2.349 3.040 nonbonded pdb=" N GLU A 259 " pdb=" OE1 GLU A 259 " model vdw 2.371 3.120 nonbonded pdb=" O ASN B 3 " pdb=" NH2 ARG C 83 " model vdw 2.393 3.120 ... (remaining 60625 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.120 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.006 0.056 7802 Z= 0.358 Angle : 0.699 10.611 10588 Z= 0.425 Chirality : 0.047 0.295 1096 Planarity : 0.005 0.060 1334 Dihedral : 14.184 87.231 2925 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.97 (0.29), residues: 875 helix: 1.67 (0.30), residues: 307 sheet: 1.01 (0.41), residues: 166 loop : -0.29 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 94 HIS 0.007 0.001 HIS A 353 PHE 0.015 0.002 PHE A 70 TYR 0.018 0.002 TYR B 111 ARG 0.007 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8067 (mtmt) REVERT: E 74 CYS cc_start: 0.8814 (m) cc_final: 0.8455 (m) outliers start: 0 outliers final: 1 residues processed: 143 average time/residue: 1.2695 time to fit residues: 191.1872 Evaluate side-chains 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 229 ASN B 3 ASN C 41 GLN D 70 GLN E 27 HIS E 68 HIS E 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.095199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.061771 restraints weight = 18630.541| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.11 r_work: 0.2885 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7802 Z= 0.213 Angle : 0.637 10.208 10588 Z= 0.330 Chirality : 0.044 0.193 1096 Planarity : 0.005 0.046 1334 Dihedral : 6.550 59.754 1089 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.13 % Allowed : 9.65 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 875 helix: 1.93 (0.31), residues: 311 sheet: 1.09 (0.40), residues: 167 loop : -0.31 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS B 73 PHE 0.014 0.001 PHE D 25 TYR 0.019 0.001 TYR E 83 ARG 0.010 0.001 ARG D 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8102 (pmm150) cc_final: 0.7666 (pmm150) REVERT: A 228 HIS cc_start: 0.8514 (t-90) cc_final: 0.7998 (t70) REVERT: A 229 ASN cc_start: 0.8422 (m-40) cc_final: 0.8146 (m-40) REVERT: B 14 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7663 (p0) REVERT: B 122 LYS cc_start: 0.7892 (mmtm) cc_final: 0.7322 (mtpt) REVERT: C 116 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8827 (mt) REVERT: D 8 ARG cc_start: 0.7037 (mtp85) cc_final: 0.6753 (mtp180) REVERT: E 17 MET cc_start: 0.7186 (ttp) cc_final: 0.6985 (tmm) REVERT: E 33 ARG cc_start: 0.7382 (mtp85) cc_final: 0.6754 (ttp-170) outliers start: 17 outliers final: 5 residues processed: 116 average time/residue: 1.2938 time to fit residues: 158.7394 Evaluate side-chains 107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN C 14 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059998 restraints weight = 19222.522| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.14 r_work: 0.2837 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7802 Z= 0.347 Angle : 0.651 11.333 10588 Z= 0.335 Chirality : 0.043 0.180 1096 Planarity : 0.004 0.059 1334 Dihedral : 6.540 58.770 1086 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.63 % Allowed : 11.28 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.21 (0.29), residues: 875 helix: 2.03 (0.31), residues: 311 sheet: 1.13 (0.40), residues: 164 loop : -0.30 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.004 0.001 HIS B 28 PHE 0.014 0.002 PHE B 112 TYR 0.016 0.002 TYR B 111 ARG 0.009 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7813 (mmmm) REVERT: C 20 LYS cc_start: 0.7916 (tppt) cc_final: 0.7632 (tptp) REVERT: C 116 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8840 (mt) REVERT: C 136 ASP cc_start: 0.8536 (t0) cc_final: 0.8335 (OUTLIER) REVERT: D 8 ARG cc_start: 0.7365 (mtp85) cc_final: 0.7136 (mtp180) REVERT: D 26 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9358 (pt0) REVERT: E 17 MET cc_start: 0.7671 (ttp) cc_final: 0.7444 (ppp) REVERT: E 20 LYS cc_start: 0.7738 (tttp) cc_final: 0.7510 (tptm) REVERT: E 33 ARG cc_start: 0.7344 (mtp85) cc_final: 0.6684 (ttp-170) outliers start: 21 outliers final: 11 residues processed: 107 average time/residue: 1.2524 time to fit residues: 141.8461 Evaluate side-chains 107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061704 restraints weight = 18884.072| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.09 r_work: 0.2889 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7802 Z= 0.184 Angle : 0.604 11.745 10588 Z= 0.306 Chirality : 0.041 0.151 1096 Planarity : 0.004 0.053 1334 Dihedral : 6.303 55.237 1086 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.63 % Allowed : 12.16 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.43 (0.29), residues: 875 helix: 2.22 (0.31), residues: 308 sheet: 1.09 (0.40), residues: 167 loop : -0.08 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.002 0.001 HIS B 139 PHE 0.014 0.001 PHE D 25 TYR 0.013 0.001 TYR B 111 ARG 0.006 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: B 14 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7698 (p0) REVERT: B 122 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7803 (mmmm) REVERT: C 116 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8856 (mt) REVERT: C 136 ASP cc_start: 0.8165 (t0) cc_final: 0.7892 (t0) REVERT: E 33 ARG cc_start: 0.7317 (mtp85) cc_final: 0.6579 (ttp-170) REVERT: E 45 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5898 (ppp) outliers start: 21 outliers final: 7 residues processed: 113 average time/residue: 1.2106 time to fit residues: 144.9161 Evaluate side-chains 105 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 84 optimal weight: 0.0170 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.095305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062322 restraints weight = 18768.848| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.09 r_work: 0.2907 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7802 Z= 0.172 Angle : 0.603 12.606 10588 Z= 0.304 Chirality : 0.041 0.146 1096 Planarity : 0.004 0.041 1334 Dihedral : 6.137 53.993 1086 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.26 % Allowed : 14.91 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.48 (0.29), residues: 875 helix: 2.22 (0.31), residues: 308 sheet: 1.09 (0.40), residues: 168 loop : -0.01 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.002 0.001 HIS A 228 PHE 0.007 0.001 PHE D 93 TYR 0.016 0.001 TYR E 83 ARG 0.009 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8166 (pmm150) cc_final: 0.7941 (pmm150) REVERT: A 237 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: B 14 ASP cc_start: 0.7976 (p0) cc_final: 0.7597 (p0) REVERT: C 116 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8897 (mt) REVERT: C 136 ASP cc_start: 0.8131 (t0) cc_final: 0.7811 (t0) REVERT: E 29 PHE cc_start: 0.7566 (m-80) cc_final: 0.7254 (m-80) outliers start: 18 outliers final: 6 residues processed: 104 average time/residue: 1.1643 time to fit residues: 128.5096 Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.095242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062577 restraints weight = 18836.566| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.05 r_work: 0.2905 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7802 Z= 0.198 Angle : 0.602 12.975 10588 Z= 0.302 Chirality : 0.041 0.146 1096 Planarity : 0.004 0.044 1334 Dihedral : 6.111 53.572 1086 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.88 % Allowed : 14.66 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.53 (0.30), residues: 875 helix: 2.27 (0.31), residues: 308 sheet: 0.91 (0.39), residues: 183 loop : 0.10 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 211 HIS 0.002 0.001 HIS E 27 PHE 0.011 0.001 PHE D 25 TYR 0.023 0.001 TYR E 83 ARG 0.008 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: B 14 ASP cc_start: 0.8001 (p0) cc_final: 0.7629 (p0) REVERT: B 122 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7519 (mmpt) REVERT: C 28 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8500 (ptmm) REVERT: C 116 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8897 (mt) REVERT: C 136 ASP cc_start: 0.8106 (t0) cc_final: 0.7796 (t70) REVERT: E 29 PHE cc_start: 0.7504 (m-80) cc_final: 0.7185 (m-80) outliers start: 23 outliers final: 9 residues processed: 106 average time/residue: 1.1346 time to fit residues: 127.8479 Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.095014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061961 restraints weight = 18802.672| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.05 r_work: 0.2900 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7802 Z= 0.203 Angle : 0.638 14.415 10588 Z= 0.319 Chirality : 0.042 0.187 1096 Planarity : 0.006 0.163 1334 Dihedral : 6.140 53.623 1086 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.26 % Allowed : 15.41 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.52 (0.30), residues: 875 helix: 2.22 (0.31), residues: 308 sheet: 0.92 (0.39), residues: 183 loop : 0.11 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.010 0.001 HIS A 228 PHE 0.012 0.001 PHE C 32 TYR 0.023 0.001 TYR E 18 ARG 0.015 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8164 (pmm150) cc_final: 0.7880 (pmm150) REVERT: A 228 HIS cc_start: 0.8326 (t70) cc_final: 0.7450 (t-170) REVERT: A 237 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: A 301 LYS cc_start: 0.8983 (mppt) cc_final: 0.8657 (mptt) REVERT: B 14 ASP cc_start: 0.8016 (p0) cc_final: 0.7636 (p0) REVERT: B 122 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7520 (mmpt) REVERT: C 116 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8899 (mt) REVERT: C 136 ASP cc_start: 0.8101 (t0) cc_final: 0.7790 (t70) REVERT: D 28 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8130 (tppt) REVERT: E 29 PHE cc_start: 0.7268 (m-80) cc_final: 0.6962 (m-80) REVERT: E 45 MET cc_start: 0.6674 (tmm) cc_final: 0.6263 (ppp) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 1.2106 time to fit residues: 129.6786 Evaluate side-chains 101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 75 optimal weight: 0.0170 chunk 53 optimal weight: 0.5980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.062859 restraints weight = 19034.309| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.11 r_work: 0.2922 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7802 Z= 0.173 Angle : 0.647 14.158 10588 Z= 0.322 Chirality : 0.041 0.231 1096 Planarity : 0.005 0.132 1334 Dihedral : 6.070 53.391 1086 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.01 % Allowed : 15.66 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.45 (0.29), residues: 875 helix: 2.13 (0.31), residues: 314 sheet: 0.86 (0.39), residues: 182 loop : 0.09 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 211 HIS 0.010 0.001 HIS A 228 PHE 0.012 0.001 PHE C 32 TYR 0.011 0.001 TYR B 111 ARG 0.010 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: B 14 ASP cc_start: 0.7938 (p0) cc_final: 0.7567 (p0) REVERT: B 122 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7503 (mmpt) REVERT: C 136 ASP cc_start: 0.8079 (t0) cc_final: 0.7767 (t70) REVERT: D 7 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8987 (mm) REVERT: D 28 LYS cc_start: 0.8681 (mmmm) cc_final: 0.8159 (tppt) REVERT: E 29 PHE cc_start: 0.7255 (m-80) cc_final: 0.6924 (m-80) REVERT: E 45 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6485 (ppp) REVERT: E 105 MET cc_start: 0.9002 (ptp) cc_final: 0.8623 (mpp) outliers start: 16 outliers final: 7 residues processed: 103 average time/residue: 1.2129 time to fit residues: 132.4496 Evaluate side-chains 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061281 restraints weight = 19204.152| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.14 r_work: 0.2885 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7802 Z= 0.232 Angle : 0.675 14.381 10588 Z= 0.338 Chirality : 0.042 0.208 1096 Planarity : 0.004 0.055 1334 Dihedral : 6.098 53.678 1086 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.63 % Allowed : 16.54 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.49 (0.29), residues: 875 helix: 2.12 (0.31), residues: 314 sheet: 1.02 (0.40), residues: 178 loop : 0.08 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.004 0.001 HIS B 28 PHE 0.012 0.001 PHE C 32 TYR 0.014 0.001 TYR B 111 ARG 0.005 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: B 14 ASP cc_start: 0.8091 (p0) cc_final: 0.7682 (p0) REVERT: B 88 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 122 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7467 (mmpt) REVERT: C 136 ASP cc_start: 0.8135 (t0) cc_final: 0.7812 (t70) REVERT: D 7 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8932 (mm) REVERT: D 28 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8088 (tppt) REVERT: E 29 PHE cc_start: 0.7247 (m-80) cc_final: 0.6900 (m-80) REVERT: E 45 MET cc_start: 0.6813 (tmm) cc_final: 0.6511 (ppp) REVERT: E 105 MET cc_start: 0.9075 (ptp) cc_final: 0.8743 (mpp) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 1.2112 time to fit residues: 128.5538 Evaluate side-chains 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.094590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061574 restraints weight = 19029.432| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.10 r_work: 0.2887 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7802 Z= 0.228 Angle : 0.686 13.716 10588 Z= 0.339 Chirality : 0.042 0.234 1096 Planarity : 0.004 0.046 1334 Dihedral : 6.088 53.735 1086 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.88 % Allowed : 16.29 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.42 (0.29), residues: 875 helix: 2.12 (0.31), residues: 314 sheet: 0.82 (0.40), residues: 175 loop : 0.09 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 211 HIS 0.003 0.001 HIS B 139 PHE 0.011 0.001 PHE C 32 TYR 0.049 0.001 TYR E 18 ARG 0.004 0.000 ARG A 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8915 (ttt) REVERT: A 237 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: B 14 ASP cc_start: 0.8062 (p0) cc_final: 0.7653 (p0) REVERT: B 88 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 99 ASP cc_start: 0.8870 (t0) cc_final: 0.8589 (t70) REVERT: B 122 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7493 (mmpt) REVERT: C 136 ASP cc_start: 0.8113 (t0) cc_final: 0.7802 (t70) REVERT: D 7 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8941 (mm) REVERT: D 28 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8040 (tppt) REVERT: E 29 PHE cc_start: 0.7215 (m-80) cc_final: 0.6961 (m-80) REVERT: E 45 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6636 (ppp) REVERT: E 105 MET cc_start: 0.9026 (ptp) cc_final: 0.8663 (mpp) outliers start: 15 outliers final: 7 residues processed: 96 average time/residue: 1.3132 time to fit residues: 133.6207 Evaluate side-chains 95 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.094532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.061666 restraints weight = 19004.231| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.06 r_work: 0.2892 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7802 Z= 0.223 Angle : 0.692 13.935 10588 Z= 0.343 Chirality : 0.042 0.262 1096 Planarity : 0.004 0.044 1334 Dihedral : 6.110 53.745 1086 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.38 % Allowed : 16.92 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.42 (0.29), residues: 875 helix: 2.08 (0.31), residues: 314 sheet: 0.86 (0.40), residues: 175 loop : 0.11 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 211 HIS 0.003 0.001 HIS B 28 PHE 0.011 0.001 PHE C 32 TYR 0.013 0.001 TYR B 111 ARG 0.007 0.000 ARG D 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6473.61 seconds wall clock time: 113 minutes 24.18 seconds (6804.18 seconds total)