Starting phenix.real_space_refine on Fri Dec 8 04:06:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/12_2023/7l0r_23101.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/12_2023/7l0r_23101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/12_2023/7l0r_23101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/12_2023/7l0r_23101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/12_2023/7l0r_23101.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/12_2023/7l0r_23101.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 53 5.16 5 C 4450 2.51 5 N 1176 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 8": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6968 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2424 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2385 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Chain: "G" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 310 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Time building chain proxies: 4.16, per 1000 atoms: 0.60 Number of scatterers: 6968 At special positions: 0 Unit cell: (75.075, 112.2, 121.275, 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 53 16.00 O 1289 8.00 N 1176 7.00 C 4450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 225 " 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: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 43.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 60 through 91 Processing helix chain 'C' and resid 100 through 129 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 137 through 173 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 182 through 202 Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.519A pdb=" N THR C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 270 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 300 through 334 Proline residue: C 323 - end of helix removed outlier: 3.533A pdb=" N ILE C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 371 Proline residue: C 366 - end of helix Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.508A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.781A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.405A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'G' and resid 32 through 48 Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.527A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.895A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.837A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.974A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.399A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.063A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.903A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1062 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: 1.83 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1875 1.33 - 1.45: 1457 1.45 - 1.57: 3699 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 7108 Sorted by residual: bond pdb=" C HIS C 133 " pdb=" N PRO C 134 " ideal model delta sigma weight residual 1.331 1.385 -0.053 1.28e-02 6.10e+03 1.72e+01 bond pdb=" N LEU B 95 " pdb=" CA LEU B 95 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.30e+00 bond pdb=" N ASP A 309 " pdb=" CA ASP A 309 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.33e-02 5.65e+03 6.36e+00 bond pdb=" N LEU C 256 " pdb=" CA LEU C 256 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.14e+00 bond pdb=" N ASP B 323 " pdb=" CA ASP B 323 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.83e+00 ... (remaining 7103 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.03: 131 106.03 - 113.06: 3725 113.06 - 120.09: 2857 120.09 - 127.12: 2830 127.12 - 134.15: 88 Bond angle restraints: 9631 Sorted by residual: angle pdb=" N PHE C 376 " pdb=" CA PHE C 376 " pdb=" C PHE C 376 " ideal model delta sigma weight residual 112.54 105.52 7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N VAL C 131 " pdb=" CA VAL C 131 " pdb=" C VAL C 131 " ideal model delta sigma weight residual 107.51 99.00 8.51 1.49e+00 4.50e-01 3.26e+01 angle pdb=" N LYS A 46 " pdb=" CA LYS A 46 " pdb=" C LYS A 46 " ideal model delta sigma weight residual 111.28 105.13 6.15 1.09e+00 8.42e-01 3.18e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.82 127.90 -7.08 1.47e+00 4.63e-01 2.32e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 ... (remaining 9626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3770 15.98 - 31.96: 329 31.96 - 47.93: 77 47.93 - 63.91: 24 63.91 - 79.89: 4 Dihedral angle restraints: 4204 sinusoidal: 1628 harmonic: 2576 Sorted by residual: dihedral pdb=" CB CYS C 142 " pdb=" SG CYS C 142 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -165.89 79.89 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CA PHE G 64 " pdb=" C PHE G 64 " pdb=" N LYS G 65 " pdb=" CA LYS G 65 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 4201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 836 0.082 - 0.164: 221 0.164 - 0.246: 41 0.246 - 0.328: 13 0.328 - 0.410: 1 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA HIS C 133 " pdb=" N HIS C 133 " pdb=" C HIS C 133 " pdb=" CB HIS C 133 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB VAL C 266 " pdb=" CA VAL C 266 " pdb=" CG1 VAL C 266 " pdb=" CG2 VAL C 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1109 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 374 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C ALA C 374 " -0.092 2.00e-02 2.50e+03 pdb=" O ALA C 374 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN C 375 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 49 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG B 49 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG B 49 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 50 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 300 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.01e+01 pdb=" C VAL C 300 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL C 300 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 301 " -0.018 2.00e-02 2.50e+03 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 201 2.66 - 3.22: 6562 3.22 - 3.78: 11590 3.78 - 4.34: 14908 4.34 - 4.90: 24418 Nonbonded interactions: 57679 Sorted by model distance: nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.106 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.232 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 2.440 nonbonded pdb=" N GLU A 43 " pdb=" OE1 GLU A 43 " model vdw 2.286 2.520 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.304 2.440 ... (remaining 57674 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.900 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 : 0.007 0.081 7108 Z= 0.479 Angle : 1.372 10.325 9631 Z= 0.787 Chirality : 0.079 0.410 1112 Planarity : 0.008 0.058 1209 Dihedral : 13.578 70.468 2535 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.05 % Allowed : 11.26 % Favored : 87.70 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.24), residues: 869 helix: -1.98 (0.20), residues: 376 sheet: -2.25 (0.36), residues: 173 loop : -2.41 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP B 297 HIS 0.008 0.003 HIS A 188 PHE 0.038 0.004 PHE C 376 TYR 0.029 0.004 TYR C 349 ARG 0.012 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 301 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 306 average time/residue: 0.2354 time to fit residues: 89.8010 Evaluate side-chains 201 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0662 time to fit residues: 1.4372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 159 ASN C 219 HIS C 239 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7108 Z= 0.200 Angle : 0.696 8.070 9631 Z= 0.367 Chirality : 0.045 0.207 1112 Planarity : 0.005 0.040 1209 Dihedral : 5.405 28.638 955 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 869 helix: -0.38 (0.23), residues: 381 sheet: -1.43 (0.35), residues: 176 loop : -2.39 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 339 HIS 0.015 0.002 HIS A 195 PHE 0.039 0.002 PHE C 246 TYR 0.018 0.002 TYR C 369 ARG 0.006 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.2091 time to fit residues: 72.4992 Evaluate side-chains 184 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.0670 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN C 239 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 88 ASN B 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7108 Z= 0.169 Angle : 0.650 7.320 9631 Z= 0.340 Chirality : 0.044 0.147 1112 Planarity : 0.004 0.042 1209 Dihedral : 4.927 21.736 955 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.26 % Allowed : 4.58 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 869 helix: 0.40 (0.25), residues: 379 sheet: -0.96 (0.36), residues: 174 loop : -2.30 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.023 0.002 PHE C 344 TYR 0.016 0.001 TYR C 349 ARG 0.006 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 256 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 256 average time/residue: 0.2014 time to fit residues: 67.0935 Evaluate side-chains 185 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0939 time to fit residues: 1.1939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 HIS ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS A 52 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7108 Z= 0.226 Angle : 0.670 7.181 9631 Z= 0.351 Chirality : 0.045 0.156 1112 Planarity : 0.004 0.045 1209 Dihedral : 4.920 16.916 955 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.26 % Allowed : 3.80 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.28), residues: 869 helix: 0.84 (0.26), residues: 377 sheet: -0.81 (0.37), residues: 180 loop : -1.95 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.026 0.002 PHE C 344 TYR 0.018 0.002 TYR B 59 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 239 average time/residue: 0.1765 time to fit residues: 56.1916 Evaluate side-chains 171 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 230 ASN B 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7108 Z= 0.254 Angle : 0.686 7.085 9631 Z= 0.362 Chirality : 0.045 0.146 1112 Planarity : 0.004 0.045 1209 Dihedral : 4.938 18.090 955 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.28), residues: 869 helix: 1.05 (0.27), residues: 377 sheet: -0.64 (0.38), residues: 179 loop : -1.81 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 297 HIS 0.007 0.001 HIS B 225 PHE 0.027 0.002 PHE C 344 TYR 0.017 0.002 TYR C 349 ARG 0.010 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1913 time to fit residues: 56.2629 Evaluate side-chains 166 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.0970 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7108 Z= 0.190 Angle : 0.657 7.088 9631 Z= 0.341 Chirality : 0.045 0.193 1112 Planarity : 0.004 0.046 1209 Dihedral : 4.872 19.494 955 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.26 % Allowed : 3.27 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 869 helix: 1.20 (0.27), residues: 375 sheet: -0.37 (0.39), residues: 181 loop : -1.65 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 258 HIS 0.004 0.001 HIS B 311 PHE 0.025 0.002 PHE C 344 TYR 0.018 0.002 TYR C 349 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 225 average time/residue: 0.1867 time to fit residues: 55.9345 Evaluate side-chains 164 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1016 time to fit residues: 1.2692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 52 GLN B 91 HIS B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7108 Z= 0.187 Angle : 0.672 8.346 9631 Z= 0.346 Chirality : 0.045 0.169 1112 Planarity : 0.005 0.055 1209 Dihedral : 4.808 18.245 955 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.26 % Allowed : 1.83 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.29), residues: 869 helix: 1.18 (0.27), residues: 376 sheet: -0.29 (0.38), residues: 180 loop : -1.61 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.025 0.002 PHE C 344 TYR 0.017 0.001 TYR B 85 ARG 0.013 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 228 average time/residue: 0.1749 time to fit residues: 53.8660 Evaluate side-chains 165 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0940 time to fit residues: 1.1844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 159 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 311 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7108 Z= 0.396 Angle : 0.828 9.040 9631 Z= 0.433 Chirality : 0.049 0.156 1112 Planarity : 0.006 0.057 1209 Dihedral : 5.501 21.562 955 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 27.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.39 % Allowed : 2.36 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.28), residues: 869 helix: 0.93 (0.26), residues: 380 sheet: -0.73 (0.37), residues: 183 loop : -1.64 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 82 HIS 0.005 0.001 HIS C 269 PHE 0.030 0.003 PHE C 344 TYR 0.024 0.003 TYR C 62 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 211 average time/residue: 0.1723 time to fit residues: 49.7919 Evaluate side-chains 161 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0994 time to fit residues: 1.2411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN C 325 HIS A 204 GLN A 213 HIS A 304 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7108 Z= 0.208 Angle : 0.721 8.652 9631 Z= 0.373 Chirality : 0.046 0.182 1112 Planarity : 0.005 0.058 1209 Dihedral : 5.040 18.345 955 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.13 % Allowed : 0.52 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 869 helix: 1.03 (0.26), residues: 377 sheet: -0.50 (0.38), residues: 173 loop : -1.57 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.005 0.001 HIS B 225 PHE 0.025 0.002 PHE C 128 TYR 0.032 0.002 TYR C 154 ARG 0.013 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1840 time to fit residues: 54.3447 Evaluate side-chains 162 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 0.0770 chunk 78 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 213 HIS A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7108 Z= 0.209 Angle : 0.724 9.021 9631 Z= 0.374 Chirality : 0.046 0.168 1112 Planarity : 0.005 0.061 1209 Dihedral : 4.987 21.146 955 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.29), residues: 869 helix: 0.96 (0.26), residues: 384 sheet: -0.48 (0.39), residues: 174 loop : -1.52 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.034 0.002 PHE C 246 TYR 0.032 0.002 TYR C 154 ARG 0.014 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1697 time to fit residues: 48.1095 Evaluate side-chains 156 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN C 325 HIS A 213 HIS A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.110443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089848 restraints weight = 21082.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092429 restraints weight = 12578.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094156 restraints weight = 8687.193| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7108 Z= 0.233 Angle : 0.739 8.181 9631 Z= 0.380 Chirality : 0.046 0.178 1112 Planarity : 0.005 0.063 1209 Dihedral : 5.013 21.389 955 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 869 helix: 0.96 (0.26), residues: 384 sheet: -0.50 (0.38), residues: 183 loop : -1.54 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS B 225 PHE 0.027 0.002 PHE C 344 TYR 0.031 0.002 TYR C 154 ARG 0.014 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.11 seconds wall clock time: 35 minutes 14.58 seconds (2114.58 seconds total)