Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 19:11:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/04_2023/8hii_34817.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/04_2023/8hii_34817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/04_2023/8hii_34817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/04_2023/8hii_34817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/04_2023/8hii_34817.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/04_2023/8hii_34817.pdb" } resolution = 3.57 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= 0.001 sd= 0.017 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 5284 2.51 5 N 1372 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8212 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 4.75, per 1000 atoms: 0.58 Number of scatterers: 8212 At special positions: 0 Unit cell: (66.34, 101.65, 150.87, 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 1530 8.00 N 1372 7.00 C 5284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 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: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 40.8% alpha, 22.0% 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 -80 through -64 Processing helix chain 'A' and resid -58 through -43 removed outlier: 3.785A pdb=" N ALA A -54 " --> pdb=" O GLN A -58 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A -43 " --> pdb=" O ALA A -47 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -33 removed outlier: 4.211A pdb=" N ASP A -33 " --> pdb=" O PRO A -37 " (cutoff:3.500A) Processing helix chain 'A' and resid -25 through -3 removed outlier: 3.805A pdb=" N ARG A -21 " --> pdb=" O MET A -25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A -3 " --> pdb=" O LEU A -7 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.793A pdb=" N LEU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 38 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.828A pdb=" N VAL A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.702A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.755A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.685A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.736A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.108A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 Processing helix chain 'A' and resid 333 through 354 removed outlier: 4.657A pdb=" N LEU A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 338 " --> pdb=" O TRP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.845A pdb=" N ALA A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 427 through 451 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.508A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.889A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.530A pdb=" N ASP N 90 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.967A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.543A pdb=" N ASP L 187 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR L 188 " --> pdb=" O LYS L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.785A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.134A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.134A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.237A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.154A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.612A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR N 110 " --> pdb=" O ILE N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.594A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.594A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.679A pdb=" N ASN L 139 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 147 through 148 removed outlier: 3.668A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 151 through 152 438 hydrogen bonds defined for protein. 1233 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: 2.48 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2560 1.34 - 1.46: 2052 1.46 - 1.58: 3763 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8413 Sorted by residual: bond pdb=" C VAL A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.97e+00 bond pdb=" C LYS H 215 " pdb=" N PRO H 216 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.32e+00 bond pdb=" CA LYS L 185 " pdb=" C LYS L 185 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.72e-02 3.38e+03 3.75e+00 bond pdb=" C SER L 8 " pdb=" N PRO L 9 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C THR A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.25e-02 6.40e+03 2.45e+00 ... (remaining 8408 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.02: 236 107.02 - 113.77: 4613 113.77 - 120.53: 3320 120.53 - 127.28: 3180 127.28 - 134.03: 95 Bond angle restraints: 11444 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 118.52 -8.71 2.21e+00 2.05e-01 1.55e+01 angle pdb=" C ASN L 212 " pdb=" N ARG L 213 " pdb=" CA ARG L 213 " ideal model delta sigma weight residual 121.70 127.96 -6.26 1.80e+00 3.09e-01 1.21e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C PHE N 103 " pdb=" N TYR N 104 " pdb=" CA TYR N 104 " ideal model delta sigma weight residual 122.46 126.93 -4.47 1.41e+00 5.03e-01 1.01e+01 angle pdb=" CA GLU H 108 " pdb=" C GLU H 108 " pdb=" N PRO H 109 " ideal model delta sigma weight residual 118.44 123.03 -4.59 1.59e+00 3.96e-01 8.33e+00 ... (remaining 11439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 4753 15.22 - 30.44: 149 30.44 - 45.65: 44 45.65 - 60.87: 0 60.87 - 76.09: 11 Dihedral angle restraints: 4957 sinusoidal: 1880 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 169.09 -76.09 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASN A -61 " pdb=" C ASN A -61 " pdb=" N ALA A -60 " pdb=" CA ALA A -60 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 936 0.049 - 0.097: 283 0.097 - 0.146: 68 0.146 - 0.194: 7 0.194 - 0.243: 2 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 134 " pdb=" CA ILE A 134 " pdb=" CG1 ILE A 134 " pdb=" CG2 ILE A 134 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1293 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.015 2.00e-02 2.50e+03 1.39e-02 4.83e+00 pdb=" CG TRP H 102 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.033 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO H 109 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO L 60 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.025 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1930 2.79 - 3.32: 7029 3.32 - 3.84: 13294 3.84 - 4.37: 14915 4.37 - 4.90: 26285 Nonbonded interactions: 63453 Sorted by model distance: nonbonded pdb=" OG SER A 168 " pdb=" O GLY A 307 " model vdw 2.260 2.440 nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.316 2.440 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.345 2.440 nonbonded pdb=" O ASP L 187 " pdb=" OH TYR L 194 " model vdw 2.350 2.440 nonbonded pdb=" O TRP H 111 " pdb=" OH TYR L 92 " model vdw 2.351 2.440 ... (remaining 63448 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 7.250 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 0.052 8413 Z= 0.230 Angle : 0.803 9.205 11444 Z= 0.432 Chirality : 0.048 0.243 1296 Planarity : 0.006 0.049 1435 Dihedral : 9.451 75.332 2970 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -3.43 (0.21), residues: 1045 helix: -1.94 (0.20), residues: 374 sheet: -1.97 (0.29), residues: 262 loop : -2.61 (0.27), residues: 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.848 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2098 time to fit residues: 68.5092 Evaluate side-chains 204 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN A 5 GLN A 172 GLN A 277 ASN A 293 ASN A 386 GLN A 431 GLN H 42 GLN ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8413 Z= 0.291 Angle : 0.620 8.765 11444 Z= 0.324 Chirality : 0.043 0.162 1296 Planarity : 0.004 0.039 1435 Dihedral : 4.635 20.861 1153 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -1.70 (0.25), residues: 1045 helix: -0.00 (0.25), residues: 386 sheet: -1.19 (0.32), residues: 245 loop : -2.11 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 0.942 Fit side-chains outliers start: 27 outliers final: 12 residues processed: 226 average time/residue: 0.2184 time to fit residues: 65.9174 Evaluate side-chains 205 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0781 time to fit residues: 3.0488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 75 optimal weight: 0.0050 overall best weight: 0.1930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN A -20 HIS ** A -12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 8413 Z= 0.156 Angle : 0.570 9.356 11444 Z= 0.284 Chirality : 0.041 0.128 1296 Planarity : 0.003 0.031 1435 Dihedral : 4.317 17.585 1153 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -1.03 (0.26), residues: 1045 helix: 0.74 (0.27), residues: 386 sheet: -0.95 (0.32), residues: 255 loop : -1.87 (0.31), residues: 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 207 time to evaluate : 0.954 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 214 average time/residue: 0.2128 time to fit residues: 61.1499 Evaluate side-chains 205 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 196 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0736 time to fit residues: 2.4616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.0040 chunk 27 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN ** A -12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN H 169 ASN L 149 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8413 Z= 0.200 Angle : 0.571 8.632 11444 Z= 0.288 Chirality : 0.042 0.216 1296 Planarity : 0.003 0.029 1435 Dihedral : 4.261 19.340 1153 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.63 (0.27), residues: 1045 helix: 1.03 (0.27), residues: 388 sheet: -0.69 (0.33), residues: 245 loop : -1.62 (0.31), residues: 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 0.859 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 191 average time/residue: 0.2287 time to fit residues: 57.9691 Evaluate side-chains 199 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1026 time to fit residues: 3.1984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN A 277 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8413 Z= 0.165 Angle : 0.560 8.525 11444 Z= 0.279 Chirality : 0.042 0.259 1296 Planarity : 0.003 0.030 1435 Dihedral : 4.102 18.686 1153 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.34 (0.27), residues: 1045 helix: 1.28 (0.27), residues: 388 sheet: -0.54 (0.34), residues: 245 loop : -1.47 (0.32), residues: 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 0.862 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 199 average time/residue: 0.2337 time to fit residues: 61.8521 Evaluate side-chains 203 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0890 time to fit residues: 1.5290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN A -12 GLN A 277 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8413 Z= 0.200 Angle : 0.580 9.557 11444 Z= 0.288 Chirality : 0.042 0.255 1296 Planarity : 0.003 0.031 1435 Dihedral : 4.094 18.216 1153 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.17 (0.27), residues: 1045 helix: 1.44 (0.27), residues: 388 sheet: -0.46 (0.33), residues: 253 loop : -1.39 (0.33), residues: 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 201 average time/residue: 0.2225 time to fit residues: 59.6908 Evaluate side-chains 201 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1144 time to fit residues: 2.6803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.0870 chunk 57 optimal weight: 0.0770 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.0270 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A -42 GLN A -12 GLN A 277 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8413 Z= 0.183 Angle : 0.593 9.647 11444 Z= 0.291 Chirality : 0.042 0.261 1296 Planarity : 0.003 0.031 1435 Dihedral : 4.069 18.253 1153 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 (0.27), residues: 1045 helix: 1.56 (0.27), residues: 388 sheet: -0.37 (0.33), residues: 253 loop : -1.34 (0.33), residues: 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 193 average time/residue: 0.2365 time to fit residues: 60.7852 Evaluate side-chains 195 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1766 time to fit residues: 3.0776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A -42 GLN A 277 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8413 Z= 0.267 Angle : 0.645 11.438 11444 Z= 0.318 Chirality : 0.044 0.291 1296 Planarity : 0.004 0.032 1435 Dihedral : 4.298 18.130 1153 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.06 (0.27), residues: 1045 helix: 1.47 (0.27), residues: 388 sheet: -0.32 (0.34), residues: 245 loop : -1.31 (0.32), residues: 412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 200 average time/residue: 0.2336 time to fit residues: 62.2328 Evaluate side-chains 199 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 194 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1459 time to fit residues: 2.4041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 93 optimal weight: 0.0670 chunk 61 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.1274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A -42 GLN A 277 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 8413 Z= 0.154 Angle : 0.627 12.144 11444 Z= 0.302 Chirality : 0.042 0.276 1296 Planarity : 0.003 0.032 1435 Dihedral : 4.090 18.525 1153 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 (0.27), residues: 1045 helix: 1.57 (0.27), residues: 389 sheet: -0.13 (0.34), residues: 245 loop : -1.18 (0.33), residues: 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 191 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 193 average time/residue: 0.2395 time to fit residues: 61.5244 Evaluate side-chains 197 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1852 time to fit residues: 2.7806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.0040 chunk 65 optimal weight: 0.0770 chunk 87 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 overall best weight: 0.1168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN L 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8413 Z= 0.152 Angle : 0.624 12.642 11444 Z= 0.299 Chirality : 0.042 0.286 1296 Planarity : 0.004 0.035 1435 Dihedral : 3.975 18.748 1153 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.24 (0.28), residues: 1045 helix: 1.56 (0.27), residues: 391 sheet: -0.01 (0.34), residues: 252 loop : -1.10 (0.34), residues: 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.2319 time to fit residues: 59.4452 Evaluate side-chains 190 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0944 time to fit residues: 1.4837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.3980 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.0030 chunk 4 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 overall best weight: 0.1528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN ** A 293 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.138222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121222 restraints weight = 13210.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124859 restraints weight = 6688.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127264 restraints weight = 4092.583| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8413 Z= 0.160 Angle : 0.640 12.651 11444 Z= 0.303 Chirality : 0.043 0.279 1296 Planarity : 0.004 0.039 1435 Dihedral : 3.923 18.622 1153 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.29 (0.28), residues: 1045 helix: 1.54 (0.27), residues: 391 sheet: 0.08 (0.35), residues: 246 loop : -1.03 (0.33), residues: 408 =============================================================================== Job complete usr+sys time: 2091.87 seconds wall clock time: 38 minutes 31.94 seconds (2311.94 seconds total)