Starting phenix.real_space_refine on Tue Feb 13 15:21:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsw_30848/02_2024/7dsw_30848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsw_30848/02_2024/7dsw_30848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsw_30848/02_2024/7dsw_30848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsw_30848/02_2024/7dsw_30848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsw_30848/02_2024/7dsw_30848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsw_30848/02_2024/7dsw_30848_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4584 2.51 5 N 1012 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 100": "NH1" <-> "NH2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6720 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain: "A" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 3, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 3, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 56 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C10 LBN B 601 " occ=0.00 ... (7 atoms not shown) pdb=" C7 LBN B 601 " occ=0.00 residue: pdb=" C35 LBN B 602 " occ=0.00 ... (7 atoms not shown) pdb=" C5 LBN B 602 " occ=0.00 residue: pdb=" C11 LBN B 603 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN B 603 " occ=0.00 residue: pdb=" C11 LBN B 604 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN B 604 " occ=0.00 residue: pdb=" C11 LBN B 605 " occ=0.00 ... (4 atoms not shown) pdb=" C23 LBN B 605 " occ=0.00 residue: pdb=" C11 LBN B 606 " occ=0.00 ... (11 atoms not shown) pdb=" C8 LBN B 606 " occ=0.00 residue: pdb=" C11 LBN A 801 " occ=0.00 ... (11 atoms not shown) pdb=" C8 LBN A 801 " occ=0.00 residue: pdb=" C10 LBN A 802 " occ=0.00 ... (7 atoms not shown) pdb=" C7 LBN A 802 " occ=0.00 residue: pdb=" C35 LBN A 803 " occ=0.00 ... (7 atoms not shown) pdb=" C5 LBN A 803 " occ=0.00 residue: pdb=" C11 LBN A 804 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN A 804 " occ=0.00 residue: pdb=" C11 LBN A 805 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN A 805 " occ=0.00 residue: pdb=" C11 LBN A 806 " occ=0.00 ... (4 atoms not shown) pdb=" C23 LBN A 806 " occ=0.00 Time building chain proxies: 4.28, per 1000 atoms: 0.64 Number of scatterers: 6720 At special positions: 0 Unit cell: (113.36, 67.6, 68.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1098 8.00 N 1012 7.00 C 4584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 0 sheets defined 69.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 101 through 120 Processing helix chain 'B' and resid 131 through 149 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 183 through 214 removed outlier: 3.821A pdb=" N LEU B 186 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLY B 187 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 189 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 193 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 194 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 195 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B 196 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 203 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 204 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.728A pdb=" N LEU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.868A pdb=" N ALA B 244 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 280 removed outlier: 3.607A pdb=" N ILE B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 322 removed outlier: 3.673A pdb=" N PHE B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 348 removed outlier: 3.833A pdb=" N PHE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 373 through 403 Processing helix chain 'B' and resid 411 through 436 Processing helix chain 'B' and resid 446 through 453 Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.754A pdb=" N ASP B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 504' Processing helix chain 'A' and resid 101 through 120 Processing helix chain 'A' and resid 131 through 149 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 183 through 214 removed outlier: 3.820A pdb=" N LEU A 186 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A 187 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 193 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 194 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 195 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 196 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 203 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 204 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.728A pdb=" N LEU A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.868A pdb=" N ALA A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 280 removed outlier: 3.607A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 322 removed outlier: 3.673A pdb=" N PHE A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 348 removed outlier: 3.834A pdb=" N PHE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 373 through 403 Processing helix chain 'A' and resid 411 through 436 Processing helix chain 'A' and resid 446 through 453 Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.753A pdb=" N ASP A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 504' 414 hydrogen bonds defined for protein. 1110 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: 1.76 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1951 1.34 - 1.46: 1348 1.46 - 1.57: 3551 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 6892 Sorted by residual: bond pdb=" C41 LBN B 606 " pdb=" C42 LBN B 606 " ideal model delta sigma weight residual 1.497 1.568 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 LBN B 603 " pdb=" C8 LBN B 603 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C41 LBN A 801 " pdb=" C42 LBN A 801 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C5 LBN A 804 " pdb=" C8 LBN A 804 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C41 LBN A 803 " pdb=" C42 LBN A 803 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 6887 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.57: 104 105.57 - 112.72: 3850 112.72 - 119.86: 2232 119.86 - 127.00: 3085 127.00 - 134.14: 79 Bond angle restraints: 9350 Sorted by residual: angle pdb=" N ILE B 125 " pdb=" CA ILE B 125 " pdb=" C ILE B 125 " ideal model delta sigma weight residual 113.71 108.01 5.70 9.50e-01 1.11e+00 3.60e+01 angle pdb=" N ILE A 125 " pdb=" CA ILE A 125 " pdb=" C ILE A 125 " ideal model delta sigma weight residual 113.71 108.01 5.70 9.50e-01 1.11e+00 3.60e+01 angle pdb=" CA TRP B 386 " pdb=" CB TRP B 386 " pdb=" CG TRP B 386 " ideal model delta sigma weight residual 113.60 119.18 -5.58 1.90e+00 2.77e-01 8.62e+00 angle pdb=" CA TRP A 386 " pdb=" CB TRP A 386 " pdb=" CG TRP A 386 " ideal model delta sigma weight residual 113.60 119.17 -5.57 1.90e+00 2.77e-01 8.61e+00 angle pdb=" CB MET A 208 " pdb=" CG MET A 208 " pdb=" SD MET A 208 " ideal model delta sigma weight residual 112.70 121.49 -8.79 3.00e+00 1.11e-01 8.59e+00 ... (remaining 9345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 3398 14.86 - 29.72: 388 29.72 - 44.59: 106 44.59 - 59.45: 18 59.45 - 74.31: 10 Dihedral angle restraints: 3920 sinusoidal: 1512 harmonic: 2408 Sorted by residual: dihedral pdb=" CA TYR A 366 " pdb=" C TYR A 366 " pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA TYR B 366 " pdb=" C TYR B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASN B 252 " pdb=" C ASN B 252 " pdb=" N GLU B 253 " pdb=" CA GLU B 253 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 650 0.033 - 0.067: 306 0.067 - 0.100: 120 0.100 - 0.134: 36 0.134 - 0.167: 8 Chirality restraints: 1120 Sorted by residual: chirality pdb=" CA PRO B 167 " pdb=" N PRO B 167 " pdb=" C PRO B 167 " pdb=" CB PRO B 167 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA PRO A 167 " pdb=" N PRO A 167 " pdb=" C PRO A 167 " pdb=" CB PRO A 167 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CB THR A 124 " pdb=" CA THR A 124 " pdb=" OG1 THR A 124 " pdb=" CG2 THR A 124 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1117 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 445 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 446 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 446 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 446 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 445 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 446 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 446 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 446 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 161 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C PHE B 161 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE B 161 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE B 162 " 0.010 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1198 2.76 - 3.29: 6782 3.29 - 3.83: 11489 3.83 - 4.36: 12928 4.36 - 4.90: 23234 Nonbonded interactions: 55631 Sorted by model distance: nonbonded pdb=" O ARG A 440 " pdb=" NZ LYS A 443 " model vdw 2.222 2.520 nonbonded pdb=" O ARG B 440 " pdb=" NZ LYS B 443 " model vdw 2.224 2.520 nonbonded pdb=" O VAL A 494 " pdb=" OG1 THR A 498 " model vdw 2.228 2.440 nonbonded pdb=" O VAL B 494 " pdb=" OG1 THR B 498 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR B 445 " pdb=" OD1 ASP B 448 " model vdw 2.292 2.440 ... (remaining 55626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 87 through 506 or resid 802 or (resid 803 and (name C40 or \ name C41 or name C42 or name C5 )) or resid 804 or (resid 805 through 806 and ( \ name C11 or name C14 or name C17 or name C20 or name C22 or name C23)))) selection = (chain 'B' and (resid 87 through 506 or resid 602 or (resid 603 and (name C40 or \ name C41 or name C42 or name C5 )) or resid 604 through 605 or (resid 606 and ( \ name C11 or name C14 or name C17 or name C20 or name C22 or name C23)))) } 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=0.00 max=1.00 mean=0.98 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.790 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.930 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.008 0.071 6892 Z= 0.503 Angle : 0.896 8.793 9350 Z= 0.457 Chirality : 0.047 0.167 1120 Planarity : 0.005 0.049 1122 Dihedral : 14.346 74.310 2376 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.11 % Allowed : 0.00 % Favored : 98.89 % 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: -0.48 (0.29), residues: 836 helix: 0.58 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -3.35 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 386 HIS 0.007 0.001 HIS A 250 PHE 0.020 0.002 PHE A 176 TYR 0.014 0.002 TYR A 274 ARG 0.009 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 0.786 Fit side-chains REVERT: B 335 PHE cc_start: 0.8217 (m-80) cc_final: 0.7778 (m-80) REVERT: B 416 SER cc_start: 0.8889 (t) cc_final: 0.8542 (t) REVERT: B 457 LEU cc_start: 0.8142 (pp) cc_final: 0.7920 (pp) REVERT: B 476 MET cc_start: 0.7118 (mmt) cc_final: 0.6904 (pmm) REVERT: A 416 SER cc_start: 0.8891 (t) cc_final: 0.8536 (t) outliers start: 8 outliers final: 0 residues processed: 158 average time/residue: 0.1596 time to fit residues: 34.9893 Evaluate side-chains 128 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 227 ASN B 250 HIS A 220 ASN A 227 ASN A 250 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6892 Z= 0.255 Angle : 0.593 6.114 9350 Z= 0.313 Chirality : 0.043 0.211 1120 Planarity : 0.005 0.046 1122 Dihedral : 8.113 67.664 958 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.49 % Allowed : 8.31 % Favored : 89.20 % 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: -0.39 (0.29), residues: 836 helix: 0.80 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -3.53 (0.35), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.002 PHE B 295 TYR 0.018 0.002 TYR B 96 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 0.775 Fit side-chains REVERT: B 208 MET cc_start: 0.8051 (mmm) cc_final: 0.7837 (mmm) REVERT: B 247 GLU cc_start: 0.7801 (pm20) cc_final: 0.7570 (pm20) REVERT: B 416 SER cc_start: 0.8787 (t) cc_final: 0.8331 (t) REVERT: B 435 PHE cc_start: 0.8279 (t80) cc_final: 0.8059 (t80) REVERT: A 208 MET cc_start: 0.8123 (mmm) cc_final: 0.7908 (mmm) REVERT: A 247 GLU cc_start: 0.7782 (pm20) cc_final: 0.7529 (pm20) REVERT: A 416 SER cc_start: 0.8766 (t) cc_final: 0.8308 (t) REVERT: A 435 PHE cc_start: 0.8200 (t80) cc_final: 0.7994 (t80) outliers start: 18 outliers final: 13 residues processed: 146 average time/residue: 0.1492 time to fit residues: 30.7090 Evaluate side-chains 133 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 227 ASN B 250 HIS A 220 ASN A 227 ASN A 250 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6892 Z= 0.196 Angle : 0.562 6.029 9350 Z= 0.297 Chirality : 0.042 0.223 1120 Planarity : 0.005 0.044 1122 Dihedral : 7.238 65.532 958 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.22 % Allowed : 12.33 % Favored : 85.46 % 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: -0.31 (0.30), residues: 836 helix: 0.82 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -3.60 (0.35), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 386 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.001 PHE B 295 TYR 0.014 0.001 TYR B 96 ARG 0.006 0.001 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.744 Fit side-chains REVERT: B 335 PHE cc_start: 0.8017 (m-80) cc_final: 0.7695 (m-80) REVERT: B 435 PHE cc_start: 0.8253 (t80) cc_final: 0.7845 (t80) REVERT: A 278 GLU cc_start: 0.8012 (tt0) cc_final: 0.7547 (mt-10) REVERT: A 335 PHE cc_start: 0.8038 (m-80) cc_final: 0.7631 (m-80) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.1451 time to fit residues: 27.9824 Evaluate side-chains 130 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 8 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN B 250 HIS A 227 ASN A 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6892 Z= 0.171 Angle : 0.540 5.955 9350 Z= 0.285 Chirality : 0.041 0.230 1120 Planarity : 0.004 0.043 1122 Dihedral : 6.575 64.774 958 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.94 % Allowed : 14.54 % Favored : 83.52 % 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: 0.04 (0.30), residues: 836 helix: 1.07 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -3.44 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 386 HIS 0.004 0.001 HIS A 325 PHE 0.019 0.001 PHE B 295 TYR 0.012 0.001 TYR B 96 ARG 0.003 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.754 Fit side-chains REVERT: B 227 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8228 (m110) REVERT: B 278 GLU cc_start: 0.8001 (tt0) cc_final: 0.7493 (mt-10) REVERT: B 335 PHE cc_start: 0.7904 (m-80) cc_final: 0.7611 (m-80) REVERT: B 384 LYS cc_start: 0.8535 (tppt) cc_final: 0.8235 (mmtt) REVERT: A 278 GLU cc_start: 0.7967 (tt0) cc_final: 0.7544 (mt-10) REVERT: A 335 PHE cc_start: 0.7971 (m-80) cc_final: 0.7592 (m-80) REVERT: A 384 LYS cc_start: 0.8565 (tppt) cc_final: 0.8216 (mmtt) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 0.1567 time to fit residues: 28.3579 Evaluate side-chains 129 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 470 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN B 250 HIS A 227 ASN A 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6892 Z= 0.223 Angle : 0.544 5.959 9350 Z= 0.286 Chirality : 0.042 0.248 1120 Planarity : 0.004 0.045 1122 Dihedral : 6.607 66.312 958 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.19 % Allowed : 15.51 % Favored : 81.30 % 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: 0.22 (0.30), residues: 836 helix: 1.14 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -3.07 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 386 HIS 0.005 0.001 HIS A 325 PHE 0.021 0.001 PHE B 295 TYR 0.011 0.001 TYR A 274 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.630 Fit side-chains REVERT: B 227 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8238 (m110) REVERT: B 278 GLU cc_start: 0.8093 (tt0) cc_final: 0.7595 (mt-10) REVERT: B 335 PHE cc_start: 0.7983 (m-80) cc_final: 0.7646 (m-80) REVERT: A 227 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8236 (m110) REVERT: A 278 GLU cc_start: 0.8098 (tt0) cc_final: 0.7644 (mt-10) REVERT: A 335 PHE cc_start: 0.8014 (m-80) cc_final: 0.7625 (m-80) outliers start: 23 outliers final: 18 residues processed: 134 average time/residue: 0.1308 time to fit residues: 25.7763 Evaluate side-chains 138 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN B 250 HIS A 227 ASN A 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6892 Z= 0.262 Angle : 0.561 5.916 9350 Z= 0.295 Chirality : 0.042 0.250 1120 Planarity : 0.005 0.046 1122 Dihedral : 6.804 67.220 958 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.16 % Allowed : 16.20 % Favored : 79.64 % 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: 0.14 (0.30), residues: 836 helix: 1.14 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -3.22 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 386 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.002 PHE A 295 TYR 0.012 0.001 TYR B 283 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 0.794 Fit side-chains REVERT: B 208 MET cc_start: 0.7811 (mmm) cc_final: 0.7464 (tpp) REVERT: B 227 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8385 (m110) REVERT: B 278 GLU cc_start: 0.8124 (tt0) cc_final: 0.7704 (mt-10) REVERT: B 335 PHE cc_start: 0.8097 (m-80) cc_final: 0.7656 (m-80) REVERT: A 208 MET cc_start: 0.7840 (mmm) cc_final: 0.7463 (tpp) REVERT: A 227 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8340 (m110) REVERT: A 278 GLU cc_start: 0.8136 (tt0) cc_final: 0.7729 (mt-10) REVERT: A 335 PHE cc_start: 0.8089 (m-80) cc_final: 0.7699 (m-80) outliers start: 30 outliers final: 22 residues processed: 140 average time/residue: 0.1480 time to fit residues: 29.8207 Evaluate side-chains 140 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN B 250 HIS A 227 ASN A 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6892 Z= 0.215 Angle : 0.537 5.891 9350 Z= 0.283 Chirality : 0.042 0.253 1120 Planarity : 0.004 0.046 1122 Dihedral : 6.665 66.278 958 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.16 % Allowed : 16.07 % Favored : 79.78 % 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: 0.35 (0.30), residues: 836 helix: 1.23 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.83 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 386 HIS 0.005 0.001 HIS A 325 PHE 0.019 0.001 PHE B 295 TYR 0.010 0.001 TYR A 274 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.799 Fit side-chains REVERT: B 278 GLU cc_start: 0.8085 (tt0) cc_final: 0.7579 (mt-10) REVERT: B 299 PHE cc_start: 0.7797 (m-80) cc_final: 0.7495 (m-80) REVERT: B 335 PHE cc_start: 0.8041 (m-80) cc_final: 0.7615 (m-80) REVERT: B 356 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 278 GLU cc_start: 0.8096 (tt0) cc_final: 0.7617 (mt-10) REVERT: A 335 PHE cc_start: 0.8002 (m-80) cc_final: 0.7651 (m-80) REVERT: A 356 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8436 (tt) outliers start: 30 outliers final: 24 residues processed: 142 average time/residue: 0.1349 time to fit residues: 27.9284 Evaluate side-chains 149 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 40 optimal weight: 0.0980 chunk 7 optimal weight: 0.0970 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.003 0.033 6892 Z= 0.163 Angle : 0.524 5.833 9350 Z= 0.279 Chirality : 0.042 0.267 1120 Planarity : 0.004 0.045 1122 Dihedral : 6.238 63.400 958 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.60 % Allowed : 17.31 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 836 helix: 1.52 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -2.76 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.004 0.001 HIS A 325 PHE 0.017 0.001 PHE B 295 TYR 0.009 0.001 TYR A 96 ARG 0.004 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.798 Fit side-chains REVERT: B 208 MET cc_start: 0.7452 (mmm) cc_final: 0.7071 (mmm) REVERT: B 278 GLU cc_start: 0.7960 (tt0) cc_final: 0.7462 (mt-10) REVERT: B 299 PHE cc_start: 0.7760 (m-80) cc_final: 0.7430 (m-80) REVERT: B 335 PHE cc_start: 0.8067 (m-80) cc_final: 0.7711 (m-80) REVERT: B 356 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8440 (tt) REVERT: B 435 PHE cc_start: 0.8112 (t80) cc_final: 0.7787 (t80) REVERT: A 208 MET cc_start: 0.7479 (mmm) cc_final: 0.7062 (mmm) REVERT: A 217 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6643 (mp0) REVERT: A 299 PHE cc_start: 0.7785 (m-80) cc_final: 0.7431 (m-80) REVERT: A 335 PHE cc_start: 0.8070 (m-80) cc_final: 0.7751 (m-80) REVERT: A 356 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8453 (tt) outliers start: 26 outliers final: 17 residues processed: 139 average time/residue: 0.1406 time to fit residues: 28.4446 Evaluate side-chains 139 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 470 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 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 250 HIS A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6892 Z= 0.227 Angle : 0.564 6.394 9350 Z= 0.299 Chirality : 0.043 0.273 1120 Planarity : 0.005 0.046 1122 Dihedral : 6.503 66.127 958 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.74 % Allowed : 17.73 % Favored : 78.53 % 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: 0.55 (0.30), residues: 836 helix: 1.48 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 386 HIS 0.005 0.001 HIS A 325 PHE 0.019 0.001 PHE B 295 TYR 0.010 0.001 TYR A 274 ARG 0.005 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.761 Fit side-chains REVERT: B 278 GLU cc_start: 0.8070 (tt0) cc_final: 0.7592 (mt-10) REVERT: B 299 PHE cc_start: 0.7769 (m-80) cc_final: 0.7473 (m-80) REVERT: B 335 PHE cc_start: 0.8176 (m-80) cc_final: 0.7750 (m-80) REVERT: B 356 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 278 GLU cc_start: 0.8089 (tt0) cc_final: 0.7595 (mt-10) REVERT: A 356 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8461 (tt) outliers start: 27 outliers final: 23 residues processed: 133 average time/residue: 0.1375 time to fit residues: 26.8397 Evaluate side-chains 143 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 470 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6892 Z= 0.277 Angle : 0.594 6.206 9350 Z= 0.314 Chirality : 0.044 0.274 1120 Planarity : 0.005 0.046 1122 Dihedral : 6.911 67.863 958 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.74 % Allowed : 18.01 % Favored : 78.25 % 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: 0.28 (0.30), residues: 836 helix: 1.08 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.72 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.002 PHE B 295 TYR 0.013 0.002 TYR A 283 ARG 0.004 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.876 Fit side-chains REVERT: B 278 GLU cc_start: 0.8115 (tt0) cc_final: 0.7694 (mt-10) REVERT: B 299 PHE cc_start: 0.7791 (m-80) cc_final: 0.7490 (m-80) REVERT: B 335 PHE cc_start: 0.8251 (m-80) cc_final: 0.7822 (m-80) REVERT: B 356 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 382 PHE cc_start: 0.7297 (t80) cc_final: 0.6995 (t80) REVERT: B 435 PHE cc_start: 0.8116 (t80) cc_final: 0.7815 (t80) REVERT: A 208 MET cc_start: 0.7630 (mmm) cc_final: 0.7190 (mmm) REVERT: A 278 GLU cc_start: 0.8152 (tt0) cc_final: 0.7695 (mt-10) REVERT: A 335 PHE cc_start: 0.8011 (m-80) cc_final: 0.7714 (m-80) REVERT: A 356 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8465 (tt) outliers start: 27 outliers final: 24 residues processed: 138 average time/residue: 0.1392 time to fit residues: 27.6689 Evaluate side-chains 142 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 470 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.0050 chunk 48 optimal weight: 0.3980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105354 restraints weight = 8589.068| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.79 r_work: 0.3100 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6892 Z= 0.202 Angle : 0.555 6.401 9350 Z= 0.295 Chirality : 0.042 0.267 1120 Planarity : 0.004 0.046 1122 Dihedral : 6.641 65.566 958 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.02 % Allowed : 18.14 % Favored : 77.84 % 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: 0.50 (0.30), residues: 836 helix: 1.40 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.80 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 386 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.001 PHE A 335 TYR 0.010 0.001 TYR A 283 ARG 0.004 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1623.20 seconds wall clock time: 31 minutes 26.76 seconds (1886.76 seconds total)