Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 14:16:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sni_10258/04_2023/6sni_10258.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sni_10258/04_2023/6sni_10258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sni_10258/04_2023/6sni_10258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sni_10258/04_2023/6sni_10258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sni_10258/04_2023/6sni_10258.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sni_10258/04_2023/6sni_10258.pdb" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 4967 2.51 5 N 1156 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X ARG 129": "NH1" <-> "NH2" Residue "X ARG 167": "NH1" <-> "NH2" Residue "X ARG 250": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7510 Number of models: 1 Model: "" Number of chains: 7 Chain: "X" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3924 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain breaks: 1 Chain: "H" Number of atoms: 1687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} bond proxies already assigned to first conformer: 1725 Chain: "L" Number of atoms: 1659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1654 Chain: "X" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 163 Unusual residues: {'PTY': 5, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.09, per 1000 atoms: 0.81 Number of scatterers: 7510 At special positions: 0 Unit cell: (115.92, 86.52, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 1355 8.00 N 1156 7.00 C 4967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 314 " - pdb=" SG CYS X 515 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 42.7% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'X' and resid 41 through 53 removed outlier: 3.886A pdb=" N VAL X 47 " --> pdb=" O PHE X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 56 No H-bonds generated for 'chain 'X' and resid 54 through 56' Processing helix chain 'X' and resid 68 through 81 removed outlier: 3.749A pdb=" N ALA X 72 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN X 73 " --> pdb=" O ASP X 69 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN X 81 " --> pdb=" O MET X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 119 removed outlier: 3.674A pdb=" N ALA X 105 " --> pdb=" O PRO X 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE X 118 " --> pdb=" O ILE X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 154 removed outlier: 3.541A pdb=" N ILE X 147 " --> pdb=" O ARG X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 170 Processing helix chain 'X' and resid 172 through 185 removed outlier: 3.593A pdb=" N ALA X 179 " --> pdb=" O GLY X 175 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE X 183 " --> pdb=" O ALA X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 194 Processing helix chain 'X' and resid 199 through 217 removed outlier: 4.425A pdb=" N MET X 203 " --> pdb=" O TYR X 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR X 207 " --> pdb=" O MET X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 231 removed outlier: 3.921A pdb=" N VAL X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 237 removed outlier: 6.959A pdb=" N MET X 235 " --> pdb=" O PHE X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 253 removed outlier: 4.127A pdb=" N ALA X 245 " --> pdb=" O PRO X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 258 through 282 removed outlier: 3.904A pdb=" N LEU X 262 " --> pdb=" O ASN X 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU X 270 " --> pdb=" O ALA X 266 " (cutoff:3.500A) Proline residue: X 279 - end of helix Processing helix chain 'X' and resid 286 through 298 removed outlier: 3.596A pdb=" N ILE X 290 " --> pdb=" O GLY X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 removed outlier: 3.729A pdb=" N THR X 316 " --> pdb=" O PHE X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 321 through 325 Processing helix chain 'X' and resid 327 through 352 removed outlier: 3.647A pdb=" N LEU X 336 " --> pdb=" O GLN X 332 " (cutoff:3.500A) Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 358 through 374 removed outlier: 3.666A pdb=" N SER X 369 " --> pdb=" O ALA X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 382 through 392 Proline residue: X 388 - end of helix Processing helix chain 'X' and resid 393 through 395 No H-bonds generated for 'chain 'X' and resid 393 through 395' Processing helix chain 'X' and resid 398 through 414 Processing helix chain 'X' and resid 415 through 421 removed outlier: 3.846A pdb=" N LYS X 421 " --> pdb=" O PRO X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 424 through 440 removed outlier: 3.508A pdb=" N ALA X 429 " --> pdb=" O HIS X 425 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN X 436 " --> pdb=" O PHE X 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY X 440 " --> pdb=" O ASN X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 476 through 491 removed outlier: 3.845A pdb=" N LYS X 480 " --> pdb=" O ASN X 476 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER X 481 " --> pdb=" O VAL X 477 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE X 482 " --> pdb=" O VAL X 478 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 497 removed outlier: 3.623A pdb=" N LEU X 496 " --> pdb=" O PHE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 536 removed outlier: 3.554A pdb=" N GLY X 518 " --> pdb=" O ASN X 514 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE X 519 " --> pdb=" O CYS X 515 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE X 520 " --> pdb=" O ALA X 516 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS X 521 " --> pdb=" O VAL X 517 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU X 527 " --> pdb=" O SER X 523 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE X 534 " --> pdb=" O TYR X 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.674A pdb=" N SER H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.624A pdb=" N SER H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR H 105 " --> pdb=" O TRP H 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 105' Processing helix chain 'H' and resid 194 through 198 removed outlier: 4.024A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.299A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.584A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.985A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 58 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.912A pdb=" N TYR H 111 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.186A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.386A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.800A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.898A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 152 341 hydrogen bonds defined for protein. 947 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: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1122 1.30 - 1.44: 2314 1.44 - 1.58: 4221 1.58 - 1.72: 33 1.72 - 1.86: 47 Bond restraints: 7737 Sorted by residual: bond pdb=" CAK Y01 H2202 " pdb=" CBD Y01 H2202 " ideal model delta sigma weight residual 1.525 1.160 0.365 2.00e-02 2.50e+03 3.33e+02 bond pdb=" CAU Y01 H2202 " pdb=" CBI Y01 H2202 " ideal model delta sigma weight residual 1.530 1.166 0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAK Y01 X1606 " pdb=" CBD Y01 X1606 " ideal model delta sigma weight residual 1.525 1.162 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" CAU Y01 X1606 " pdb=" CBI Y01 X1606 " ideal model delta sigma weight residual 1.530 1.172 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" CAK Y01 H2201 " pdb=" CBD Y01 H2201 " ideal model delta sigma weight residual 1.525 1.168 0.357 2.00e-02 2.50e+03 3.18e+02 ... (remaining 7732 not shown) Histogram of bond angle deviations from ideal: 98.22 - 106.63: 272 106.63 - 115.04: 4623 115.04 - 123.45: 5322 123.45 - 131.86: 292 131.86 - 140.28: 25 Bond angle restraints: 10534 Sorted by residual: angle pdb=" CA PRO H 156 " pdb=" N PRO H 156 " pdb=" CD PRO H 156 " ideal model delta sigma weight residual 111.50 98.22 13.28 1.40e+00 5.10e-01 9.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA BSER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" N SER L 10 " pdb=" CA ASER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 angle pdb=" N SER L 10 " pdb=" CA BSER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 ... (remaining 10529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4097 17.99 - 35.98: 282 35.98 - 53.97: 92 53.97 - 71.96: 20 71.96 - 89.94: 2 Dihedral angle restraints: 4493 sinusoidal: 1774 harmonic: 2719 Sorted by residual: dihedral pdb=" CA MET X 541 " pdb=" C MET X 541 " pdb=" N LYS X 542 " pdb=" CA LYS X 542 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CB CYS X 314 " pdb=" SG CYS X 314 " pdb=" SG CYS X 515 " pdb=" CB CYS X 515 " ideal model delta sinusoidal sigma weight residual -86.00 -126.33 40.33 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA TRP X 90 " pdb=" C TRP X 90 " pdb=" N TYR X 91 " pdb=" CA TYR X 91 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 1144 0.315 - 0.631: 12 0.631 - 0.946: 3 0.946 - 1.262: 0 1.262 - 1.577: 3 Chirality restraints: 1162 Sorted by residual: chirality pdb=" CBD Y01 H2201 " pdb=" CAK Y01 H2201 " pdb=" CBF Y01 H2201 " pdb=" CBG Y01 H2201 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" CBD Y01 X1606 " pdb=" CAK Y01 X1606 " pdb=" CBF Y01 X1606 " pdb=" CBG Y01 X1606 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.57 2.00e-01 2.50e+01 6.19e+01 chirality pdb=" CBD Y01 H2202 " pdb=" CAK Y01 H2202 " pdb=" CBF Y01 H2202 " pdb=" CBG Y01 H2202 " both_signs ideal model delta sigma weight residual False 2.70 1.13 1.56 2.00e-01 2.50e+01 6.11e+01 ... (remaining 1159 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 278 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO X 279 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO X 279 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO X 279 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 193 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO H 194 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 194 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 194 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE X 384 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO X 385 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO X 385 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO X 385 " 0.020 5.00e-02 4.00e+02 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 102 2.62 - 3.19: 6680 3.19 - 3.76: 10613 3.76 - 4.33: 16211 4.33 - 4.90: 27373 Nonbonded interactions: 60979 Sorted by model distance: nonbonded pdb=" O LYS X 380 " pdb=" OG1 THR X 381 " model vdw 2.044 2.440 nonbonded pdb=" CE1 TYR H 154 " pdb=" OE2 GLU H 157 " model vdw 2.057 3.340 nonbonded pdb=" O THR H 140 " pdb=" OG SER H 195 " model vdw 2.201 2.440 nonbonded pdb=" O GLN L 126 " pdb=" OG SER L 129 " model vdw 2.201 2.440 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.206 2.520 ... (remaining 60974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 6.330 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.400 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 : 0.020 0.365 7737 Z= 1.341 Angle : 1.038 16.368 10534 Z= 0.549 Chirality : 0.106 1.577 1162 Planarity : 0.004 0.039 1275 Dihedral : 14.149 89.944 2744 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.23 % Favored : 90.55 % Rotamer Outliers : 8.07 % 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: -4.21 (0.23), residues: 917 helix: -2.35 (0.22), residues: 343 sheet: -1.68 (0.35), residues: 193 loop : -3.79 (0.25), residues: 381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 111 time to evaluate : 0.814 Fit side-chains outliers start: 65 outliers final: 33 residues processed: 167 average time/residue: 0.7731 time to fit residues: 140.2997 Evaluate side-chains 113 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 2 average time/residue: 0.1377 time to fit residues: 1.5000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 171 GLN X 213 ASN X 317 ASN H 13 GLN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS L 201 GLN L 212 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7737 Z= 0.213 Angle : 0.651 9.817 10534 Z= 0.326 Chirality : 0.044 0.156 1162 Planarity : 0.006 0.084 1275 Dihedral : 10.048 59.523 1133 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 6.09 % 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: -2.35 (0.27), residues: 917 helix: -0.43 (0.28), residues: 353 sheet: -0.85 (0.36), residues: 201 loop : -3.14 (0.28), residues: 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 88 time to evaluate : 0.844 Fit side-chains outliers start: 49 outliers final: 31 residues processed: 131 average time/residue: 0.8474 time to fit residues: 120.1747 Evaluate side-chains 112 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 3 average time/residue: 0.6981 time to fit residues: 3.4162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 75 HIS X 213 ASN X 291 HIS X 378 HIS H 13 GLN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 7737 Z= 0.432 Angle : 0.725 9.184 10534 Z= 0.367 Chirality : 0.048 0.160 1162 Planarity : 0.006 0.079 1275 Dihedral : 9.889 59.425 1133 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 6.09 % 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: -1.97 (0.27), residues: 917 helix: -0.23 (0.28), residues: 357 sheet: -0.54 (0.37), residues: 198 loop : -2.89 (0.30), residues: 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 80 time to evaluate : 0.844 Fit side-chains outliers start: 49 outliers final: 29 residues processed: 121 average time/residue: 0.8693 time to fit residues: 114.1452 Evaluate side-chains 112 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 1.1860 time to fit residues: 4.8480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 30.0000 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 213 ASN H 13 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7737 Z= 0.195 Angle : 0.597 8.602 10534 Z= 0.303 Chirality : 0.042 0.147 1162 Planarity : 0.006 0.077 1275 Dihedral : 8.985 59.423 1133 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 5.34 % 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: -1.36 (0.28), residues: 917 helix: 0.34 (0.29), residues: 356 sheet: -0.23 (0.37), residues: 200 loop : -2.59 (0.31), residues: 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 85 time to evaluate : 0.807 Fit side-chains outliers start: 43 outliers final: 32 residues processed: 123 average time/residue: 0.7937 time to fit residues: 106.4737 Evaluate side-chains 115 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.2086 time to fit residues: 1.7055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 0.0060 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 213 ASN X 289 ASN H 13 GLN H 76 ASN H 180 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 7737 Z= 0.200 Angle : 0.573 7.869 10534 Z= 0.293 Chirality : 0.042 0.151 1162 Planarity : 0.006 0.078 1275 Dihedral : 8.413 58.987 1133 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 5.34 % 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: -1.00 (0.29), residues: 917 helix: 0.59 (0.29), residues: 357 sheet: -0.04 (0.37), residues: 201 loop : -2.38 (0.32), residues: 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 0.899 Fit side-chains outliers start: 43 outliers final: 28 residues processed: 126 average time/residue: 0.8439 time to fit residues: 115.4060 Evaluate side-chains 112 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 1.5677 time to fit residues: 2.8104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.0070 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 7737 Z= 0.213 Angle : 0.582 8.141 10534 Z= 0.297 Chirality : 0.042 0.150 1162 Planarity : 0.006 0.078 1275 Dihedral : 8.223 58.147 1133 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 5.34 % 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: -0.86 (0.29), residues: 917 helix: 0.70 (0.29), residues: 357 sheet: 0.07 (0.38), residues: 201 loop : -2.31 (0.32), residues: 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 84 time to evaluate : 0.902 Fit side-chains outliers start: 43 outliers final: 32 residues processed: 122 average time/residue: 0.7958 time to fit residues: 105.9658 Evaluate side-chains 115 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 3 average time/residue: 0.5192 time to fit residues: 2.9152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 86 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.0980 chunk 53 optimal weight: 0.0030 chunk 34 optimal weight: 0.0870 chunk 51 optimal weight: 0.9980 overall best weight: 0.0846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 213 ASN ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN L 79 GLN L 102 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.073 7737 Z= 0.139 Angle : 0.524 8.208 10534 Z= 0.266 Chirality : 0.040 0.151 1162 Planarity : 0.005 0.076 1275 Dihedral : 7.507 59.321 1133 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 4.60 % 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: -0.29 (0.29), residues: 917 helix: 1.44 (0.29), residues: 343 sheet: 0.34 (0.38), residues: 190 loop : -2.07 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 0.851 Fit side-chains outliers start: 37 outliers final: 25 residues processed: 121 average time/residue: 0.6913 time to fit residues: 91.9166 Evaluate side-chains 101 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 1.0277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 213 ASN ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 180 GLN L 79 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 7737 Z= 0.208 Angle : 0.571 8.593 10534 Z= 0.293 Chirality : 0.041 0.156 1162 Planarity : 0.006 0.080 1275 Dihedral : 7.634 58.757 1133 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 4.47 % 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: -0.28 (0.29), residues: 917 helix: 1.34 (0.29), residues: 348 sheet: 0.36 (0.38), residues: 201 loop : -2.09 (0.32), residues: 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 77 time to evaluate : 0.823 Fit side-chains outliers start: 36 outliers final: 29 residues processed: 112 average time/residue: 0.8408 time to fit residues: 102.2677 Evaluate side-chains 107 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 2 average time/residue: 0.2067 time to fit residues: 1.6379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 0.0980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 378 HIS H 76 ASN H 180 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 7737 Z= 0.160 Angle : 0.539 8.552 10534 Z= 0.276 Chirality : 0.040 0.145 1162 Planarity : 0.006 0.076 1275 Dihedral : 7.466 58.309 1133 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 4.10 % 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: -0.12 (0.29), residues: 917 helix: 1.46 (0.29), residues: 350 sheet: 0.55 (0.38), residues: 190 loop : -2.00 (0.32), residues: 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 0.902 Fit side-chains outliers start: 33 outliers final: 28 residues processed: 110 average time/residue: 0.7768 time to fit residues: 94.4248 Evaluate side-chains 101 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 2 average time/residue: 0.1528 time to fit residues: 1.5874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 186 GLN ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 378 HIS H 76 ASN L 79 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 7737 Z= 0.317 Angle : 0.635 9.045 10534 Z= 0.325 Chirality : 0.044 0.150 1162 Planarity : 0.006 0.079 1275 Dihedral : 8.043 59.746 1133 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 4.10 % 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: -0.37 (0.29), residues: 917 helix: 1.09 (0.28), residues: 348 sheet: 0.40 (0.38), residues: 203 loop : -2.01 (0.32), residues: 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 0.883 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 111 average time/residue: 0.9455 time to fit residues: 113.2619 Evaluate side-chains 104 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 1.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.0070 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 0.0170 chunk 9 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 213 ASN ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 180 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133403 restraints weight = 17732.957| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.74 r_work: 0.3372 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.083 7737 Z= 0.155 Angle : 0.545 10.833 10534 Z= 0.279 Chirality : 0.040 0.143 1162 Planarity : 0.006 0.076 1275 Dihedral : 7.473 59.355 1133 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 3.60 % 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: 0.04 (0.29), residues: 917 helix: 1.66 (0.29), residues: 340 sheet: 0.62 (0.38), residues: 189 loop : -1.86 (0.32), residues: 388 =============================================================================== Job complete usr+sys time: 2757.19 seconds wall clock time: 49 minutes 57.88 seconds (2997.88 seconds total)