Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:08:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b01_15775/04_2023/8b01_15775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b01_15775/04_2023/8b01_15775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b01_15775/04_2023/8b01_15775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b01_15775/04_2023/8b01_15775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b01_15775/04_2023/8b01_15775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b01_15775/04_2023/8b01_15775_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.011 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 P 2 5.49 5 S 33 5.16 5 Na 2 4.78 5 C 3682 2.51 5 N 834 2.21 5 O 925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 131": "OD1" <-> "OD2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 103": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5478 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1257 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3208 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 404} Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 90 Unusual residues: {'D10': 1, 'OCT': 1, 'PTY': 1, 'TWT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {' NA': 2, 'D10': 1, 'HEX': 1, 'OCT': 5, 'PTY': 1, 'TRD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" C1 OCT A 201 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT A 201 " occ=0.50 residue: pdb=" C1 PTY A 202 " occ=0.50 ... (48 atoms not shown) pdb=" P1 PTY A 202 " occ=0.50 residue: pdb=" C1 TWT A 203 " occ=0.50 ... (20 atoms not shown) pdb=" C9 TWT A 203 " occ=0.50 residue: pdb=" C1 D10 A 204 " occ=0.50 ... (8 atoms not shown) pdb=" C9 D10 A 204 " occ=0.50 residue: pdb=" C1 OCT B 503 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 503 " occ=0.50 residue: pdb=" C1 OCT B 504 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 504 " occ=0.50 residue: pdb=" C1 OCT B 505 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 505 " occ=0.50 residue: pdb=" C1 OCT B 506 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 506 " occ=0.50 residue: pdb=" C1 OCT B 507 " occ=0.50 ... (6 atoms not shown) pdb=" C8 OCT B 507 " occ=0.50 residue: pdb=" C1 TRD B 508 " occ=0.50 ... (11 atoms not shown) pdb=" C9 TRD B 508 " occ=0.50 residue: pdb=" C1 D10 B 509 " occ=0.50 ... (8 atoms not shown) pdb=" C9 D10 B 509 " occ=0.50 residue: pdb=" C1 PTY B 510 " occ=0.50 ... (35 atoms not shown) pdb=" P1 PTY B 510 " occ=0.50 residue: pdb=" C1 HEX B 511 " occ=0.50 ... (4 atoms not shown) pdb=" C6 HEX B 511 " occ=0.50 Time building chain proxies: 3.64, per 1000 atoms: 0.66 Number of scatterers: 5478 At special positions: 0 Unit cell: (91.258, 77.082, 92.144, 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) S 33 16.00 P 2 15.00 Na 2 11.00 O 925 8.00 N 834 7.00 C 3682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 812.1 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 2 sheets defined 67.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 9 through 34 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 42 through 63 removed outlier: 3.866A pdb=" N GLY A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 79 through 110 removed outlier: 3.864A pdb=" N LEU A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 151 removed outlier: 4.717A pdb=" N ALA A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.655A pdb=" N PHE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 18 through 32 Processing helix chain 'B' and resid 36 through 49 removed outlier: 3.644A pdb=" N ASN B 39 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA B 42 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 48 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 69 removed outlier: 3.531A pdb=" N VAL B 57 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 58 - end of helix Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 109 through 127 removed outlier: 4.821A pdb=" N GLN B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.855A pdb=" N CYS B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLY B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 165 through 194 removed outlier: 4.005A pdb=" N ALA B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 216 through 229 removed outlier: 3.685A pdb=" N LEU B 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 220 " --> pdb=" O SER B 217 " (cutoff:3.500A) Proline residue: B 221 - end of helix removed outlier: 3.538A pdb=" N ILE B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 226 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 229 " --> pdb=" O GLY B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 251 Processing helix chain 'B' and resid 259 through 293 removed outlier: 3.740A pdb=" N MET B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 306 removed outlier: 4.028A pdb=" N ILE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.932A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 338 through 348 Proline residue: B 343 - end of helix removed outlier: 3.719A pdb=" N VAL B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 removed outlier: 4.179A pdb=" N LEU B 368 " --> pdb=" O MET B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 387 through 397 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 399 through 410 Processing helix chain 'B' and resid 413 through 422 removed outlier: 4.971A pdb=" N LEU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing sheet with id= A, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.620A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.655A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 861 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: 1.38 Time building geometry restraints manager: 2.34 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: 847 1.32 - 1.45: 1431 1.45 - 1.57: 3249 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 5588 Sorted by residual: bond pdb=" C GLY B 231 " pdb=" N LYS B 232 " ideal model delta sigma weight residual 1.334 1.284 0.050 1.46e-02 4.69e+03 1.17e+01 bond pdb=" N VAL B 283 " pdb=" CA VAL B 283 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.33e+00 bond pdb=" N TYR C 107 " pdb=" CA TYR C 107 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.71e+00 bond pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.48e+00 bond pdb=" CA TYR C 105 " pdb=" C TYR C 105 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.32e-02 5.74e+03 6.25e+00 ... (remaining 5583 not shown) Histogram of bond angle deviations from ideal: 92.68 - 100.94: 23 100.94 - 109.20: 303 109.20 - 117.46: 3820 117.46 - 125.72: 3314 125.72 - 133.98: 74 Bond angle restraints: 7534 Sorted by residual: angle pdb=" N PRO C 104 " pdb=" CA PRO C 104 " pdb=" C PRO C 104 " ideal model delta sigma weight residual 113.40 106.04 7.36 1.34e+00 5.57e-01 3.02e+01 angle pdb=" N PHE B 102 " pdb=" CA PHE B 102 " pdb=" C PHE B 102 " ideal model delta sigma weight residual 112.54 107.68 4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" N LEU B 321 " pdb=" CA LEU B 321 " pdb=" C LEU B 321 " ideal model delta sigma weight residual 111.14 106.89 4.25 1.08e+00 8.57e-01 1.55e+01 angle pdb=" N TYR A 128 " pdb=" CA TYR A 128 " pdb=" C TYR A 128 " ideal model delta sigma weight residual 113.15 108.69 4.46 1.19e+00 7.06e-01 1.41e+01 angle pdb=" CA TYR C 101 " pdb=" C TYR C 101 " pdb=" O TYR C 101 " ideal model delta sigma weight residual 121.49 117.51 3.98 1.16e+00 7.43e-01 1.18e+01 ... (remaining 7529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.60: 2893 14.60 - 29.19: 291 29.19 - 43.79: 86 43.79 - 58.39: 15 58.39 - 72.98: 5 Dihedral angle restraints: 3290 sinusoidal: 1334 harmonic: 1956 Sorted by residual: dihedral pdb=" CA PHE B 233 " pdb=" C PHE B 233 " pdb=" N THR B 234 " pdb=" CA THR B 234 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 131 " pdb=" CB ASP B 131 " pdb=" CG ASP B 131 " pdb=" OD1 ASP B 131 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CG ARG C 71 " pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " ideal model delta sinusoidal sigma weight residual 90.00 134.72 -44.72 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 3287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 699 0.051 - 0.102: 151 0.102 - 0.153: 27 0.153 - 0.203: 3 0.203 - 0.254: 2 Chirality restraints: 882 Sorted by residual: chirality pdb=" CA LEU B 321 " pdb=" N LEU B 321 " pdb=" C LEU B 321 " pdb=" CB LEU B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO C 104 " pdb=" N PRO C 104 " pdb=" C PRO C 104 " pdb=" CB PRO C 104 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LEU B 322 " pdb=" N LEU B 322 " pdb=" C LEU B 322 " pdb=" CB LEU B 322 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 879 not shown) Planarity restraints: 901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 105 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C TYR C 105 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR C 105 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR C 106 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 127 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 127 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 127 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 128 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 234 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO B 235 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " 0.026 5.00e-02 4.00e+02 ... (remaining 898 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 821 2.75 - 3.29: 5276 3.29 - 3.83: 8564 3.83 - 4.36: 9570 4.36 - 4.90: 17755 Nonbonded interactions: 41986 Sorted by model distance: nonbonded pdb=" OD1 ASP B 351 " pdb=" OH TYR B 425 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O TYR C 98 " model vdw 2.228 2.440 nonbonded pdb=" O GLY B 145 " pdb="NA NA B 501 " model vdw 2.282 2.470 nonbonded pdb=" NH1 ARG A 32 " pdb=" OE2 GLU B 237 " model vdw 2.302 2.520 nonbonded pdb=" NE2 GLN C 39 " pdb=" O LYS C 43 " model vdw 2.311 2.520 ... (remaining 41981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 5.580 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.500 Find NCS groups from input model: 0.150 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.004 0.050 5588 Z= 0.267 Angle : 0.598 7.359 7534 Z= 0.362 Chirality : 0.043 0.254 882 Planarity : 0.005 0.047 901 Dihedral : 13.046 72.985 2039 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.16 (0.33), residues: 678 helix: 2.35 (0.25), residues: 457 sheet: -0.48 (0.96), residues: 33 loop : -0.54 (0.43), residues: 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.604 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 0.2428 time to fit residues: 33.1786 Evaluate side-chains 82 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 HIS B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5588 Z= 0.188 Angle : 0.513 7.057 7534 Z= 0.264 Chirality : 0.038 0.146 882 Planarity : 0.005 0.048 901 Dihedral : 7.188 59.530 867 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.05 (0.33), residues: 678 helix: 2.20 (0.25), residues: 459 sheet: -0.76 (0.95), residues: 34 loop : -0.36 (0.42), residues: 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.611 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.2087 time to fit residues: 22.4689 Evaluate side-chains 82 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1507 time to fit residues: 1.4168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5588 Z= 0.178 Angle : 0.484 7.078 7534 Z= 0.247 Chirality : 0.037 0.143 882 Planarity : 0.004 0.047 901 Dihedral : 7.056 59.988 867 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.05 (0.33), residues: 678 helix: 2.26 (0.25), residues: 456 sheet: -1.30 (0.87), residues: 34 loop : -0.37 (0.42), residues: 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.565 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.2003 time to fit residues: 21.0850 Evaluate side-chains 80 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0508 time to fit residues: 1.1535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5588 Z= 0.264 Angle : 0.520 7.577 7534 Z= 0.265 Chirality : 0.039 0.143 882 Planarity : 0.005 0.047 901 Dihedral : 7.271 58.320 867 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.90 (0.33), residues: 678 helix: 2.12 (0.25), residues: 459 sheet: -1.27 (0.89), residues: 34 loop : -0.41 (0.43), residues: 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.621 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.1941 time to fit residues: 19.8775 Evaluate side-chains 81 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1169 time to fit residues: 1.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5588 Z= 0.214 Angle : 0.501 8.056 7534 Z= 0.253 Chirality : 0.038 0.139 882 Planarity : 0.005 0.047 901 Dihedral : 7.166 58.997 867 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.93 (0.33), residues: 678 helix: 2.18 (0.25), residues: 458 sheet: -1.31 (0.91), residues: 34 loop : -0.49 (0.43), residues: 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.630 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.1927 time to fit residues: 19.6547 Evaluate side-chains 78 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0562 time to fit residues: 0.8789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5588 Z= 0.209 Angle : 0.490 7.266 7534 Z= 0.250 Chirality : 0.038 0.150 882 Planarity : 0.005 0.047 901 Dihedral : 7.125 59.431 867 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.91 (0.33), residues: 678 helix: 2.18 (0.25), residues: 458 sheet: -1.40 (0.91), residues: 34 loop : -0.52 (0.43), residues: 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.585 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.1929 time to fit residues: 19.6178 Evaluate side-chains 77 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3118 time to fit residues: 1.1346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5588 Z= 0.174 Angle : 0.480 6.959 7534 Z= 0.247 Chirality : 0.037 0.148 882 Planarity : 0.004 0.046 901 Dihedral : 6.986 59.430 867 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.88 (0.33), residues: 678 helix: 2.13 (0.25), residues: 465 sheet: -1.42 (0.91), residues: 34 loop : -0.54 (0.45), residues: 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.648 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.2012 time to fit residues: 20.6801 Evaluate side-chains 78 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0942 time to fit residues: 1.0099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5588 Z= 0.271 Angle : 0.524 7.600 7534 Z= 0.267 Chirality : 0.039 0.147 882 Planarity : 0.005 0.046 901 Dihedral : 7.217 59.928 867 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.82 (0.33), residues: 678 helix: 2.13 (0.25), residues: 462 sheet: -1.48 (0.92), residues: 34 loop : -0.65 (0.44), residues: 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.579 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.2023 time to fit residues: 20.4613 Evaluate side-chains 79 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0576 time to fit residues: 1.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5588 Z= 0.142 Angle : 0.479 6.584 7534 Z= 0.246 Chirality : 0.037 0.146 882 Planarity : 0.004 0.046 901 Dihedral : 6.771 57.910 867 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.89 (0.33), residues: 678 helix: 2.18 (0.24), residues: 464 sheet: -1.43 (0.92), residues: 34 loop : -0.66 (0.44), residues: 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.531 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 79 average time/residue: 0.1855 time to fit residues: 19.3371 Evaluate side-chains 78 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3204 time to fit residues: 1.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 5588 Z= 0.154 Angle : 0.482 6.680 7534 Z= 0.246 Chirality : 0.037 0.147 882 Planarity : 0.004 0.046 901 Dihedral : 6.546 57.028 867 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.90 (0.33), residues: 678 helix: 2.17 (0.25), residues: 467 sheet: -1.33 (0.92), residues: 34 loop : -0.70 (0.44), residues: 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.642 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1957 time to fit residues: 18.9025 Evaluate side-chains 75 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0538 time to fit residues: 0.8769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.088552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073692 restraints weight = 10438.883| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.64 r_work: 0.2897 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5588 Z= 0.173 Angle : 0.485 6.855 7534 Z= 0.247 Chirality : 0.037 0.146 882 Planarity : 0.004 0.046 901 Dihedral : 6.485 56.954 867 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.94 (0.33), residues: 678 helix: 2.22 (0.24), residues: 465 sheet: -1.37 (0.92), residues: 34 loop : -0.68 (0.44), residues: 179 =============================================================================== Job complete usr+sys time: 1433.32 seconds wall clock time: 26 minutes 33.03 seconds (1593.03 seconds total)