Starting phenix.real_space_refine on Mon Mar 11 05:36:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/03_2024/7n64_24193.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/03_2024/7n64_24193.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/7n64_24193/03_2024/7n64_24193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/03_2024/7n64_24193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/03_2024/7n64_24193.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/03_2024/7n64_24193.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 26 5.16 5 C 4574 2.51 5 N 1194 2.21 5 O 1395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L GLU 195": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7189 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2235 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1687 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1604 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.18, per 1000 atoms: 0.58 Number of scatterers: 7189 At special positions: 0 Unit cell: (99, 79.2, 120.45, 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 1395 8.00 N 1194 7.00 C 4574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 160 " - pdb=" SG CYS H 216 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 165 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN B 343 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 6.3% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.708A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 59 through 63 removed outlier: 3.853A pdb=" N LYS H 63 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 209 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.300A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 7.424A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.168A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 121 Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.779A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.685A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.087A pdb=" N SER H 69 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 47 through 50 removed outlier: 5.264A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR H 92 " --> pdb=" O THR H 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.506A pdb=" N LYS H 163 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR H 196 " --> pdb=" O ASP H 164 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER H 199 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 171 through 174 removed outlier: 3.833A pdb=" N TYR H 214 " --> pdb=" O VAL H 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.581A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 118 removed outlier: 4.729A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE L 139 " --> pdb=" O TYR L 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 144 through 149 187 hydrogen bonds defined for protein. 444 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: 2.17 Time building geometry restraints manager: 3.09 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: 1932 1.33 - 1.45: 1675 1.45 - 1.57: 3736 1.57 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 7375 Sorted by residual: bond pdb=" N GLN L 3 " pdb=" CA GLN L 3 " ideal model delta sigma weight residual 1.452 1.504 -0.051 1.22e-02 6.72e+03 1.76e+01 bond pdb=" C ALA L 111 " pdb=" N ALA L 112 " ideal model delta sigma weight residual 1.333 1.240 0.093 2.74e-02 1.33e+03 1.14e+01 bond pdb=" N GLN L 100 " pdb=" CA GLN L 100 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.17e-02 7.31e+03 9.83e+00 bond pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.27e-02 6.20e+03 9.03e+00 bond pdb=" N ARG A 237 " pdb=" CA ARG A 237 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.13e-02 7.83e+03 8.78e+00 ... (remaining 7370 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.70: 168 105.70 - 112.80: 3837 112.80 - 119.91: 2446 119.91 - 127.01: 3502 127.01 - 134.12: 82 Bond angle restraints: 10035 Sorted by residual: angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 117.47 123.32 -5.85 1.16e+00 7.43e-01 2.55e+01 angle pdb=" C ILE L 106 " pdb=" N LYS L 107 " pdb=" CA LYS L 107 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C TYR A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta sigma weight residual 122.10 116.05 6.05 1.66e+00 3.63e-01 1.33e+01 angle pdb=" N GLN L 124 " pdb=" CA GLN L 124 " pdb=" C GLN L 124 " ideal model delta sigma weight residual 111.07 107.30 3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N SER B 371 " pdb=" CA SER B 371 " pdb=" C SER B 371 " ideal model delta sigma weight residual 114.56 110.16 4.40 1.27e+00 6.20e-01 1.20e+01 ... (remaining 10030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.86: 3946 18.86 - 37.72: 405 37.72 - 56.58: 61 56.58 - 75.44: 25 75.44 - 94.30: 8 Dihedral angle restraints: 4445 sinusoidal: 1815 harmonic: 2630 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 149.28 -56.28 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS H 160 " pdb=" SG CYS H 160 " pdb=" SG CYS H 216 " pdb=" CB CYS H 216 " ideal model delta sinusoidal sigma weight residual 93.00 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 4442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 981 0.091 - 0.181: 121 0.181 - 0.272: 11 0.272 - 0.362: 1 0.362 - 0.453: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CB VAL A 130 " pdb=" CA VAL A 130 " pdb=" CG1 VAL A 130 " pdb=" CG2 VAL A 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1113 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 138 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO H 139 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO H 139 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 139 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 368 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C LEU B 368 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU B 368 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR B 369 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 148 " 0.015 2.00e-02 2.50e+03 1.63e-02 6.64e+00 pdb=" CG TRP L 148 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP L 148 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 148 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 148 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 148 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP L 148 " -0.000 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 553 2.71 - 3.25: 7847 3.25 - 3.80: 11838 3.80 - 4.35: 14933 4.35 - 4.90: 24653 Nonbonded interactions: 59824 Sorted by model distance: nonbonded pdb=" O ASN H 53 " pdb=" OG SER H 54 " model vdw 2.157 2.440 nonbonded pdb=" CG2 ILE L 2 " pdb=" N GLN L 3 " model vdw 2.193 3.540 nonbonded pdb=" N GLY B 404 " pdb=" O GLN B 506 " model vdw 2.205 2.520 nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.211 2.520 nonbonded pdb=" N GLN H 191 " pdb=" O LEU H 195 " model vdw 2.216 2.520 ... (remaining 59819 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: 0.740 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: 0.000 Extract box with map and model: 2.880 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.980 Find NCS groups from input model: 0.210 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 : 0.009 0.093 7375 Z= 0.576 Angle : 1.060 11.208 10035 Z= 0.586 Chirality : 0.062 0.453 1116 Planarity : 0.006 0.072 1286 Dihedral : 15.983 94.299 2735 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 36.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 20.76 % Favored : 78.91 % Rotamer: Outliers : 1.78 % Allowed : 1.40 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.80 (0.26), residues: 896 helix: -3.80 (0.50), residues: 40 sheet: -1.47 (0.32), residues: 269 loop : -3.15 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP L 148 HIS 0.008 0.002 HIS L 189 PHE 0.036 0.004 PHE B 377 TYR 0.034 0.003 TYR H 93 ARG 0.010 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7737 (ptmm) cc_final: 0.7108 (ptmm) REVERT: A 224 GLU cc_start: 0.7898 (pm20) cc_final: 0.7504 (pm20) REVERT: B 517 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6862 (tt) REVERT: L 138 ASN cc_start: 0.8587 (m110) cc_final: 0.7973 (m110) REVERT: L 192 TYR cc_start: 0.6668 (m-80) cc_final: 0.6394 (m-10) outliers start: 14 outliers final: 5 residues processed: 167 average time/residue: 0.2012 time to fit residues: 44.1379 Evaluate side-chains 127 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7375 Z= 0.271 Angle : 0.804 8.581 10035 Z= 0.411 Chirality : 0.050 0.244 1116 Planarity : 0.006 0.056 1286 Dihedral : 8.454 51.292 1130 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.50 (0.27), residues: 896 helix: -3.72 (0.48), residues: 45 sheet: -1.47 (0.31), residues: 292 loop : -2.82 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 148 HIS 0.005 0.001 HIS H 220 PHE 0.014 0.002 PHE A 106 TYR 0.036 0.002 TYR L 91 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7573 (p) cc_final: 0.6657 (p) REVERT: A 206 LYS cc_start: 0.7885 (ptmm) cc_final: 0.7427 (ptmm) REVERT: A 224 GLU cc_start: 0.7614 (pm20) cc_final: 0.7399 (pm20) REVERT: H 31 ASP cc_start: 0.7174 (m-30) cc_final: 0.6857 (m-30) REVERT: L 4 MET cc_start: 0.6787 (tpt) cc_final: 0.6338 (tpt) REVERT: L 138 ASN cc_start: 0.8538 (m110) cc_final: 0.7914 (m110) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1914 time to fit residues: 39.3521 Evaluate side-chains 120 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7375 Z= 0.274 Angle : 0.788 10.304 10035 Z= 0.401 Chirality : 0.050 0.259 1116 Planarity : 0.005 0.053 1286 Dihedral : 7.778 49.952 1130 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.34 (0.27), residues: 896 helix: -3.35 (0.55), residues: 45 sheet: -1.39 (0.31), residues: 292 loop : -2.72 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 174 HIS 0.004 0.001 HIS H 35 PHE 0.024 0.002 PHE B 347 TYR 0.029 0.002 TYR B 365 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7603 (ptmm) REVERT: A 224 GLU cc_start: 0.7572 (pm20) cc_final: 0.7305 (pm20) REVERT: B 466 ARG cc_start: 0.7780 (ttp80) cc_final: 0.6835 (ttt-90) REVERT: B 516 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7029 (tm-30) REVERT: H 31 ASP cc_start: 0.7045 (m-30) cc_final: 0.6722 (m-30) REVERT: L 4 MET cc_start: 0.6540 (tpt) cc_final: 0.6266 (tpt) REVERT: L 138 ASN cc_start: 0.8559 (m110) cc_final: 0.8045 (m110) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2048 time to fit residues: 42.3841 Evaluate side-chains 122 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7375 Z= 0.257 Angle : 0.763 8.838 10035 Z= 0.390 Chirality : 0.049 0.257 1116 Planarity : 0.005 0.049 1286 Dihedral : 7.422 49.809 1130 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.19 (0.28), residues: 896 helix: -3.14 (0.62), residues: 45 sheet: -1.33 (0.31), residues: 286 loop : -2.59 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.005 0.001 HIS L 189 PHE 0.016 0.002 PHE B 347 TYR 0.020 0.002 TYR L 192 ARG 0.003 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.6024 (mm-30) cc_final: 0.5742 (mm-30) REVERT: A 206 LYS cc_start: 0.8166 (ptmm) cc_final: 0.7632 (ptmm) REVERT: A 224 GLU cc_start: 0.7579 (pm20) cc_final: 0.7358 (pm20) REVERT: B 466 ARG cc_start: 0.7838 (ttp80) cc_final: 0.6804 (ttt-90) REVERT: B 516 GLU cc_start: 0.7266 (tm-30) cc_final: 0.7022 (tm-30) REVERT: H 19 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7863 (ttp80) REVERT: H 31 ASP cc_start: 0.7092 (m-30) cc_final: 0.6654 (m-30) REVERT: H 181 SER cc_start: 0.7652 (t) cc_final: 0.7290 (m) REVERT: L 4 MET cc_start: 0.6539 (tpt) cc_final: 0.6117 (tpt) REVERT: L 138 ASN cc_start: 0.8434 (m110) cc_final: 0.7825 (m110) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2553 time to fit residues: 50.2635 Evaluate side-chains 124 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7375 Z= 0.362 Angle : 0.815 8.970 10035 Z= 0.419 Chirality : 0.050 0.290 1116 Planarity : 0.006 0.056 1286 Dihedral : 7.643 48.827 1130 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.63 % Favored : 83.37 % Rotamer: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.34 (0.27), residues: 896 helix: -2.88 (0.67), residues: 45 sheet: -1.52 (0.31), residues: 283 loop : -2.67 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP H 174 HIS 0.004 0.001 HIS H 220 PHE 0.023 0.003 PHE H 166 TYR 0.019 0.003 TYR L 192 ARG 0.005 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.5723 (mm-30) cc_final: 0.5304 (mm-30) REVERT: A 206 LYS cc_start: 0.8156 (ptmm) cc_final: 0.7634 (ptmm) REVERT: A 224 GLU cc_start: 0.7696 (pm20) cc_final: 0.7392 (pm20) REVERT: B 427 ASP cc_start: 0.7758 (t0) cc_final: 0.7521 (t0) REVERT: B 466 ARG cc_start: 0.7857 (ttp80) cc_final: 0.6836 (ttt-90) REVERT: H 31 ASP cc_start: 0.7148 (m-30) cc_final: 0.6749 (m-30) REVERT: L 138 ASN cc_start: 0.8526 (m110) cc_final: 0.7826 (m110) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.2001 time to fit residues: 38.5516 Evaluate side-chains 119 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7375 Z= 0.233 Angle : 0.759 8.369 10035 Z= 0.385 Chirality : 0.049 0.260 1116 Planarity : 0.005 0.047 1286 Dihedral : 7.228 50.150 1130 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.05 (0.27), residues: 896 helix: -3.09 (0.70), residues: 39 sheet: -1.22 (0.31), residues: 278 loop : -2.49 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 35 HIS 0.004 0.001 HIS H 35 PHE 0.034 0.002 PHE A 58 TYR 0.033 0.002 TYR B 365 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7759 (ptmm) REVERT: A 224 GLU cc_start: 0.7628 (pm20) cc_final: 0.7300 (pm20) REVERT: B 427 ASP cc_start: 0.7646 (t0) cc_final: 0.7390 (t0) REVERT: B 466 ARG cc_start: 0.7441 (ttp80) cc_final: 0.6882 (ttt180) REVERT: H 19 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8010 (ttp80) REVERT: H 31 ASP cc_start: 0.7011 (m-30) cc_final: 0.6486 (m-30) REVERT: H 181 SER cc_start: 0.7365 (t) cc_final: 0.7049 (m) REVERT: L 4 MET cc_start: 0.6558 (tpt) cc_final: 0.6150 (tpt) REVERT: L 82 ASP cc_start: 0.7996 (m-30) cc_final: 0.7164 (m-30) REVERT: L 132 VAL cc_start: 0.8392 (t) cc_final: 0.8137 (m) REVERT: L 138 ASN cc_start: 0.8453 (m110) cc_final: 0.7758 (m110) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.2056 time to fit residues: 42.8192 Evaluate side-chains 124 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7375 Z= 0.205 Angle : 0.745 10.877 10035 Z= 0.374 Chirality : 0.048 0.229 1116 Planarity : 0.005 0.043 1286 Dihedral : 6.937 50.418 1130 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.79 (0.28), residues: 896 helix: -3.19 (0.69), residues: 39 sheet: -1.03 (0.31), residues: 284 loop : -2.31 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 35 HIS 0.004 0.001 HIS L 189 PHE 0.026 0.002 PHE B 497 TYR 0.018 0.002 TYR B 451 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7996 (ptmm) cc_final: 0.7759 (ptmm) REVERT: A 224 GLU cc_start: 0.7532 (pm20) cc_final: 0.7201 (pm20) REVERT: B 427 ASP cc_start: 0.7631 (t0) cc_final: 0.7313 (t0) REVERT: B 466 ARG cc_start: 0.7813 (ttp80) cc_final: 0.6925 (ttt180) REVERT: B 516 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6686 (tm-30) REVERT: H 19 ARG cc_start: 0.8265 (ttp80) cc_final: 0.8004 (ttp80) REVERT: H 31 ASP cc_start: 0.6960 (m-30) cc_final: 0.6391 (m-30) REVERT: H 181 SER cc_start: 0.7404 (t) cc_final: 0.7085 (m) REVERT: H 224 ASN cc_start: 0.8349 (m-40) cc_final: 0.7408 (p0) REVERT: L 4 MET cc_start: 0.6568 (tpt) cc_final: 0.6181 (tpt) REVERT: L 91 TYR cc_start: 0.6760 (p90) cc_final: 0.6164 (p90) REVERT: L 132 VAL cc_start: 0.8417 (t) cc_final: 0.8102 (m) REVERT: L 138 ASN cc_start: 0.8384 (m110) cc_final: 0.7726 (m110) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1902 time to fit residues: 41.1875 Evaluate side-chains 128 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN H 13 GLN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7375 Z= 0.303 Angle : 0.793 9.982 10035 Z= 0.401 Chirality : 0.050 0.272 1116 Planarity : 0.005 0.049 1286 Dihedral : 7.254 49.459 1130 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.93 (0.28), residues: 896 helix: -3.05 (0.73), residues: 39 sheet: -1.08 (0.32), residues: 275 loop : -2.44 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP H 174 HIS 0.006 0.001 HIS L 189 PHE 0.020 0.002 PHE B 497 TYR 0.049 0.002 TYR H 196 ARG 0.008 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8046 (ptmm) cc_final: 0.7783 (ptmm) REVERT: A 224 GLU cc_start: 0.7618 (pm20) cc_final: 0.7311 (pm20) REVERT: B 402 ILE cc_start: 0.8821 (pt) cc_final: 0.8512 (pt) REVERT: B 427 ASP cc_start: 0.7714 (t0) cc_final: 0.7431 (t0) REVERT: B 466 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7013 (ptm160) REVERT: H 19 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7829 (ttp80) REVERT: H 31 ASP cc_start: 0.7069 (m-30) cc_final: 0.6544 (m-30) REVERT: H 181 SER cc_start: 0.7442 (t) cc_final: 0.7115 (m) REVERT: H 190 LEU cc_start: 0.8462 (tp) cc_final: 0.7818 (mp) REVERT: L 91 TYR cc_start: 0.6732 (p90) cc_final: 0.6006 (p90) REVERT: L 132 VAL cc_start: 0.8428 (t) cc_final: 0.8175 (m) REVERT: L 138 ASN cc_start: 0.8423 (m110) cc_final: 0.7751 (m110) REVERT: L 185 ASP cc_start: 0.7832 (p0) cc_final: 0.7544 (p0) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.2056 time to fit residues: 41.2921 Evaluate side-chains 125 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 47 optimal weight: 0.0070 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7375 Z= 0.271 Angle : 0.781 9.223 10035 Z= 0.395 Chirality : 0.050 0.266 1116 Planarity : 0.005 0.052 1286 Dihedral : 7.178 49.772 1130 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.62 % Favored : 85.38 % Rotamer: Outliers : 0.13 % Allowed : 0.63 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.87 (0.28), residues: 896 helix: -3.11 (0.72), residues: 39 sheet: -1.02 (0.32), residues: 274 loop : -2.40 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 152 HIS 0.005 0.001 HIS L 189 PHE 0.032 0.002 PHE B 497 TYR 0.041 0.002 TYR H 196 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8000 (ptmm) cc_final: 0.7715 (ptmm) REVERT: A 224 GLU cc_start: 0.7647 (pm20) cc_final: 0.7335 (pm20) REVERT: B 427 ASP cc_start: 0.7709 (t0) cc_final: 0.7474 (t0) REVERT: B 466 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7018 (ptm160) REVERT: H 19 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7900 (ttp80) REVERT: H 31 ASP cc_start: 0.7051 (m-30) cc_final: 0.6537 (m-30) REVERT: H 181 SER cc_start: 0.7382 (t) cc_final: 0.7083 (m) REVERT: L 4 MET cc_start: 0.6479 (tpt) cc_final: 0.6061 (tpt) REVERT: L 91 TYR cc_start: 0.6731 (p90) cc_final: 0.5987 (p90) REVERT: L 132 VAL cc_start: 0.8414 (t) cc_final: 0.8153 (m) REVERT: L 138 ASN cc_start: 0.8472 (m110) cc_final: 0.7770 (m110) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1957 time to fit residues: 42.2655 Evaluate side-chains 126 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7375 Z= 0.308 Angle : 0.804 9.952 10035 Z= 0.410 Chirality : 0.050 0.275 1116 Planarity : 0.005 0.047 1286 Dihedral : 7.299 49.489 1130 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.51 % Favored : 84.49 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.85 (0.28), residues: 896 helix: -3.05 (0.73), residues: 39 sheet: -1.04 (0.31), residues: 288 loop : -2.39 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.041 0.002 PHE B 497 TYR 0.040 0.003 TYR L 192 ARG 0.007 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8048 (ptmm) cc_final: 0.7766 (ptmm) REVERT: A 224 GLU cc_start: 0.7647 (pm20) cc_final: 0.7342 (pm20) REVERT: B 427 ASP cc_start: 0.7767 (t0) cc_final: 0.7525 (t0) REVERT: H 19 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7827 (ttp80) REVERT: H 31 ASP cc_start: 0.7084 (m-30) cc_final: 0.6579 (m-30) REVERT: H 181 SER cc_start: 0.7417 (t) cc_final: 0.7149 (m) REVERT: L 4 MET cc_start: 0.6504 (tpt) cc_final: 0.6102 (tpt) REVERT: L 21 ILE cc_start: 0.6088 (tp) cc_final: 0.5840 (tp) REVERT: L 91 TYR cc_start: 0.6777 (p90) cc_final: 0.5941 (p90) REVERT: L 132 VAL cc_start: 0.8475 (t) cc_final: 0.8208 (m) REVERT: L 137 ASN cc_start: 0.7124 (t0) cc_final: 0.6104 (t0) REVERT: L 138 ASN cc_start: 0.8533 (m110) cc_final: 0.7284 (m110) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1940 time to fit residues: 40.3117 Evaluate side-chains 120 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.133614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110450 restraints weight = 17267.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.112970 restraints weight = 10177.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114590 restraints weight = 7021.576| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7375 Z= 0.246 Angle : 0.768 9.598 10035 Z= 0.391 Chirality : 0.049 0.259 1116 Planarity : 0.005 0.044 1286 Dihedral : 7.087 50.131 1130 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 0.13 % Allowed : 0.63 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.79 (0.28), residues: 896 helix: -3.11 (0.71), residues: 39 sheet: -0.98 (0.31), residues: 288 loop : -2.35 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 174 HIS 0.004 0.001 HIS L 189 PHE 0.044 0.002 PHE B 497 TYR 0.033 0.002 TYR L 192 ARG 0.007 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.30 seconds wall clock time: 32 minutes 16.54 seconds (1936.54 seconds total)