Starting phenix.real_space_refine (version: dev) on Sat Feb 18 04:18:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/02_2023/7n64_24193.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/02_2023/7n64_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_24193/02_2023/7n64_24193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/02_2023/7n64_24193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/02_2023/7n64_24193.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n64_24193/02_2023/7n64_24193.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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: 1 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 chiralities: 2 Time building chain proxies: 4.69, per 1000 atoms: 0.65 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: 3.32 Conformation dependent library (CDL) restraints added in 1.0 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: 0.37 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: 1.81 Time building geometry restraints manager: 3.36 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 - 16.06: 3741 16.06 - 32.13: 474 32.13 - 48.19: 93 48.19 - 64.25: 28 64.25 - 80.32: 10 Dihedral angle restraints: 4346 sinusoidal: 1716 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 4343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 985 0.091 - 0.181: 118 0.181 - 0.272: 10 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 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. 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: 0.570 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: 3.050 Check model and map are aligned: 0.100 Process input model: 21.970 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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= 0.568 Angle : 1.043 11.208 10035 Z= 0.585 Chirality : 0.061 0.453 1116 Planarity : 0.006 0.072 1286 Dihedral : 15.152 80.315 2636 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 % 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 *********************** 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 : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 167 average time/residue: 0.2032 time to fit residues: 44.4838 Evaluate side-chains 125 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.873 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0787 time to fit residues: 1.8356 ------------------------------------------------------------------------------- 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: 0.6999 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7375 Z= 0.272 Angle : 0.791 8.327 10035 Z= 0.410 Chirality : 0.050 0.269 1116 Planarity : 0.006 0.056 1286 Dihedral : 7.049 43.580 1031 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer Outliers : 0.13 % 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: -3.49 (0.27), residues: 896 helix: -3.73 (0.48), residues: 45 sheet: -1.46 (0.30), residues: 292 loop : -2.81 (0.26), residues: 559 *********************** 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 151 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.2000 time to fit residues: 40.2493 Evaluate side-chains 117 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0716 time to fit residues: 1.1989 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- 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** A 239 GLN B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN H 75 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 7375 Z= 0.386 Angle : 0.846 10.910 10035 Z= 0.438 Chirality : 0.052 0.310 1116 Planarity : 0.006 0.062 1286 Dihedral : 7.176 43.596 1031 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer Outliers : 0.13 % 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: -3.49 (0.27), residues: 896 helix: -3.19 (0.68), residues: 39 sheet: -1.51 (0.31), residues: 282 loop : -2.84 (0.25), residues: 575 *********************** 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 149 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 149 average time/residue: 0.2197 time to fit residues: 42.8222 Evaluate side-chains 114 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0669 time to fit residues: 1.3230 ------------------------------------------------------------------------------- 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: 20.0000 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7375 Z= 0.218 Angle : 0.753 9.082 10035 Z= 0.387 Chirality : 0.049 0.248 1116 Planarity : 0.005 0.048 1286 Dihedral : 6.602 37.029 1031 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer Outliers : 0.00 % 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: -3.22 (0.27), residues: 896 helix: -3.22 (0.59), residues: 45 sheet: -1.38 (0.31), residues: 292 loop : -2.59 (0.26), residues: 559 *********************** 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 163 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2010 time to fit residues: 43.4051 Evaluate side-chains 127 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0246 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 191 GLN ** 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 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2297 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= 0.244 Angle : 0.742 9.624 10035 Z= 0.381 Chirality : 0.048 0.256 1116 Planarity : 0.005 0.044 1286 Dihedral : 6.387 34.303 1031 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer Outliers : 0.00 % 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: -3.04 (0.27), residues: 896 helix: -3.17 (0.67), residues: 39 sheet: -1.20 (0.31), residues: 284 loop : -2.51 (0.26), residues: 573 *********************** 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 160 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2017 time to fit residues: 43.0552 Evaluate side-chains 123 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1228 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.0010 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 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 27 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7375 Z= 0.222 Angle : 0.735 8.755 10035 Z= 0.376 Chirality : 0.048 0.241 1116 Planarity : 0.005 0.042 1286 Dihedral : 6.325 31.933 1031 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer Outliers : 0.13 % 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 (0.27), residues: 896 helix: -3.87 (0.64), residues: 33 sheet: -1.10 (0.31), residues: 276 loop : -2.39 (0.25), residues: 587 *********************** 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 162 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1952 time to fit residues: 42.3372 Evaluate side-chains 125 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1412 ------------------------------------------------------------------------------- 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: 9.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ** 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** L 189 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7375 Z= 0.251 Angle : 0.747 11.018 10035 Z= 0.381 Chirality : 0.049 0.251 1116 Planarity : 0.005 0.043 1286 Dihedral : 6.276 31.577 1031 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer Outliers : 0.25 % 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: -3.10 (0.69), residues: 39 sheet: -1.06 (0.31), residues: 283 loop : -2.39 (0.26), residues: 574 *********************** 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 164 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.2082 time to fit residues: 45.3382 Evaluate side-chains 122 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1735 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 77 optimal weight: 0.0070 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 overall best weight: 1.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7375 Z= 0.221 Angle : 0.741 9.938 10035 Z= 0.377 Chirality : 0.049 0.239 1116 Planarity : 0.005 0.041 1286 Dihedral : 6.167 28.840 1031 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer Outliers : 0.00 % 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: -2.77 (0.28), residues: 896 helix: -3.28 (0.69), residues: 39 sheet: -0.98 (0.32), residues: 281 loop : -2.31 (0.26), residues: 576 *********************** 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 162 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2106 time to fit residues: 45.2629 Evaluate side-chains 121 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1990 ------------------------------------------------------------------------------- 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: 9.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.0010 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- 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** H 72 ASN ** 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** L 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7375 Z= 0.227 Angle : 0.742 10.359 10035 Z= 0.382 Chirality : 0.049 0.242 1116 Planarity : 0.005 0.041 1286 Dihedral : 6.097 27.190 1031 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer Outliers : 0.00 % 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: -2.72 (0.28), residues: 896 helix: -3.27 (0.67), residues: 39 sheet: -0.90 (0.31), residues: 274 loop : -2.28 (0.26), residues: 583 *********************** 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 154 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2067 time to fit residues: 41.9784 Evaluate side-chains 120 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1623 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 chunk 7 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- 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** ** 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** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7375 Z= 0.234 Angle : 0.754 9.978 10035 Z= 0.388 Chirality : 0.049 0.228 1116 Planarity : 0.005 0.041 1286 Dihedral : 6.141 26.515 1031 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer Outliers : 0.00 % 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: -2.75 (0.28), residues: 896 helix: -2.88 (0.66), residues: 45 sheet: -0.95 (0.31), residues: 275 loop : -2.30 (0.26), residues: 576 ********************** 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: 0 poor density : 155 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2080 time to fit residues: 43.3905 Evaluate side-chains 121 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2474 ------------------------------------------------------------------------------- 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: 8.9990 chunk 64 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.131160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108545 restraints weight = 17642.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111104 restraints weight = 10351.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112761 restraints weight = 7030.693| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 7375 Z= 0.357 Angle : 0.833 10.062 10035 Z= 0.433 Chirality : 0.052 0.303 1116 Planarity : 0.006 0.049 1286 Dihedral : 6.616 38.006 1031 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.74 % Favored : 83.26 % Rotamer Outliers : 0.13 % 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: -2.94 (0.27), residues: 896 helix: -3.12 (0.72), residues: 39 sheet: -1.07 (0.31), residues: 278 loop : -2.46 (0.25), residues: 579 =============================================================================== Job complete usr+sys time: 1628.90 seconds wall clock time: 30 minutes 46.24 seconds (1846.24 seconds total)