Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 20:08:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/07_2023/7bgy_12184_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/07_2023/7bgy_12184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/07_2023/7bgy_12184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/07_2023/7bgy_12184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/07_2023/7bgy_12184_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/07_2023/7bgy_12184_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.084 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 7043 2.51 5 N 1825 2.21 5 O 1989 1.98 5 F 4 1.80 5 H 11192 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 461": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 22119 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 10201 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "C" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2879 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 452 Classifications: {'peptide': 29} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'9Y0': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'MF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 9.76, per 1000 atoms: 0.44 Number of scatterers: 22119 At special positions: 0 Unit cell: (74.13, 97.428, 173.676, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 62 16.00 P 2 15.00 Mg 2 11.99 F 4 9.00 O 1989 8.00 N 1825 7.00 C 7043 6.00 H 11192 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "ATOM 15465 OG1 THR B 471 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.82 Conformation dependent library (CDL) restraints added in 1.9 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 55.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix removed outlier: 3.846A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.412A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.785A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 412 through 436 removed outlier: 4.361A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.038A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.601A pdb=" N ALA A 463 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 509 Proline residue: A 499 - end of helix removed outlier: 3.917A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 548 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 27 through 30 No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 62 through 85 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 245 removed outlier: 4.174A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 4.092A pdb=" N LEU B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 509 removed outlier: 3.510A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 528 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 558 through 595 Proline residue: B 592 - end of helix removed outlier: 3.986A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 603 Processing helix chain 'B' and resid 613 through 636 removed outlier: 4.530A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 3 through 24 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 Processing sheet with id= B, first strand: chain 'B' and resid 105 through 108 Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 removed outlier: 4.165A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= F, first strand: chain 'B' and resid 322 through 324 removed outlier: 6.732A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1683 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: 7.99 Time building geometry restraints manager: 19.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 11180 1.00 - 1.20: 16 1.20 - 1.41: 4301 1.41 - 1.61: 6686 1.61 - 1.81: 120 Bond restraints: 22303 Sorted by residual: bond pdb=" C13 9Y0 A 802 " pdb=" C14 9Y0 A 802 " ideal model delta sigma weight residual 1.333 1.561 -0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C21 9Y0 A 802 " pdb=" O7 9Y0 A 802 " ideal model delta sigma weight residual 1.330 1.428 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C5 9Y0 A 802 " pdb=" O5 9Y0 A 802 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C31 PEV A 801 " pdb=" O2 PEV A 801 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C14 9Y0 A 802 " pdb=" C15 9Y0 A 802 " ideal model delta sigma weight residual 1.497 1.561 -0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 22298 not shown) Histogram of bond angle deviations from ideal: 78.88 - 91.89: 4 91.89 - 104.91: 240 104.91 - 117.93: 30389 117.93 - 130.95: 9730 130.95 - 143.96: 40 Bond angle restraints: 40403 Sorted by residual: angle pdb="HD22 LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD23 LEU B 85 " ideal model delta sigma weight residual 110.00 78.88 31.12 3.00e+00 1.11e-01 1.08e+02 angle pdb="HD21 LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD22 LEU B 85 " ideal model delta sigma weight residual 110.00 80.03 29.97 3.00e+00 1.11e-01 9.98e+01 angle pdb=" CG LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD23 LEU B 85 " ideal model delta sigma weight residual 109.00 79.78 29.22 3.00e+00 1.11e-01 9.49e+01 angle pdb=" CG LEU B 85 " pdb=" CD2 LEU B 85 " pdb="HD21 LEU B 85 " ideal model delta sigma weight residual 109.00 82.69 26.31 3.00e+00 1.11e-01 7.69e+01 angle pdb=" CG ASN D 25 " pdb=" ND2 ASN D 25 " pdb="HD22 ASN D 25 " ideal model delta sigma weight residual 120.00 143.96 -23.96 3.00e+00 1.11e-01 6.38e+01 ... (remaining 40398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.09: 8445 27.09 - 54.17: 292 54.17 - 81.26: 46 81.26 - 108.35: 6 108.35 - 135.43: 2 Dihedral angle restraints: 8791 sinusoidal: 4110 harmonic: 4681 Sorted by residual: dihedral pdb=" N 9Y0 A 802 " pdb=" C3 9Y0 A 802 " pdb=" C4 9Y0 A 802 " pdb=" O1 9Y0 A 802 " ideal model delta sinusoidal sigma weight residual -62.65 72.78 -135.43 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C3 9Y0 A 802 " pdb=" O1 9Y0 A 802 " pdb=" P 9Y0 A 802 " pdb=" O3 9Y0 A 802 " ideal model delta sinusoidal sigma weight residual 291.93 172.04 119.89 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 8788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1454 0.060 - 0.120: 307 0.120 - 0.180: 42 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA ILE B 591 " pdb=" N ILE B 591 " pdb=" C ILE B 591 " pdb=" CB ILE B 591 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB THR B 516 " pdb=" CA THR B 516 " pdb=" OG1 THR B 516 " pdb=" CG2 THR B 516 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB THR A 251 " pdb=" CA THR A 251 " pdb=" OG1 THR A 251 " pdb=" CG2 THR A 251 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1805 not shown) Planarity restraints: 3292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 A 802 " 0.167 2.00e-02 2.50e+03 2.93e-01 8.60e+02 pdb=" C13 9Y0 A 802 " -0.405 2.00e-02 2.50e+03 pdb=" C14 9Y0 A 802 " 0.368 2.00e-02 2.50e+03 pdb=" C15 9Y0 A 802 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 25 " -0.054 2.00e-02 2.50e+03 9.34e-02 1.31e+02 pdb=" CG ASN D 25 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN D 25 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN D 25 " 0.160 2.00e-02 2.50e+03 pdb="HD21 ASN D 25 " 0.038 2.00e-02 2.50e+03 pdb="HD22 ASN D 25 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 93 " -0.065 2.00e-02 2.50e+03 8.82e-02 1.17e+02 pdb=" CD GLN A 93 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 93 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 93 " 0.144 2.00e-02 2.50e+03 pdb="HE21 GLN A 93 " 0.018 2.00e-02 2.50e+03 pdb="HE22 GLN A 93 " -0.140 2.00e-02 2.50e+03 ... (remaining 3289 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1791 2.21 - 2.81: 48566 2.81 - 3.41: 63250 3.41 - 4.00: 85448 4.00 - 4.60: 134243 Nonbonded interactions: 333298 Sorted by model distance: nonbonded pdb=" OD1 ASP B 473 " pdb=" H ASN B 474 " model vdw 1.615 1.850 nonbonded pdb=" OD1 ASP B 143 " pdb=" H GLY B 178 " model vdw 1.618 1.850 nonbonded pdb=" OD2 ASP B 552 " pdb=" HZ2 LYS B 557 " model vdw 1.636 1.850 nonbonded pdb=" O GLY C 61 " pdb=" HE2 HIS C 66 " model vdw 1.637 1.850 nonbonded pdb=" O ARG A 157 " pdb=" HZ3 LYS A 407 " model vdw 1.638 1.850 ... (remaining 333293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.080 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: 0.360 Extract box with map and model: 8.930 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 68.890 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.010 0.228 11111 Z= 0.623 Angle : 0.970 23.957 15099 Z= 0.471 Chirality : 0.050 0.300 1808 Planarity : 0.009 0.293 1910 Dihedral : 13.845 135.434 3978 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.19), residues: 1442 helix: -0.92 (0.16), residues: 862 sheet: -3.76 (0.41), residues: 90 loop : -2.90 (0.24), residues: 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 156 average time/residue: 2.1380 time to fit residues: 370.0542 Evaluate side-chains 122 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.3941 time to fit residues: 2.6301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11111 Z= 0.198 Angle : 0.571 5.739 15099 Z= 0.295 Chirality : 0.039 0.147 1808 Planarity : 0.004 0.041 1910 Dihedral : 9.124 145.888 1595 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.21), residues: 1442 helix: 0.22 (0.17), residues: 868 sheet: -3.51 (0.46), residues: 80 loop : -2.50 (0.24), residues: 494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 137 average time/residue: 2.1416 time to fit residues: 325.7227 Evaluate side-chains 124 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.4010 time to fit residues: 3.9266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11111 Z= 0.207 Angle : 0.531 5.646 15099 Z= 0.273 Chirality : 0.038 0.146 1808 Planarity : 0.003 0.041 1910 Dihedral : 8.499 145.195 1595 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1442 helix: 0.72 (0.17), residues: 870 sheet: -3.23 (0.48), residues: 80 loop : -2.21 (0.24), residues: 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 122 average time/residue: 2.1816 time to fit residues: 296.5787 Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 2 average time/residue: 0.3532 time to fit residues: 3.1621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11111 Z= 0.189 Angle : 0.509 6.246 15099 Z= 0.260 Chirality : 0.038 0.143 1808 Planarity : 0.003 0.035 1910 Dihedral : 8.125 146.564 1595 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1442 helix: 1.01 (0.17), residues: 871 sheet: -3.02 (0.50), residues: 80 loop : -1.94 (0.25), residues: 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 126 average time/residue: 2.0942 time to fit residues: 293.4381 Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.3843 time to fit residues: 3.1075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 0.0020 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 overall best weight: 0.5868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11111 Z= 0.172 Angle : 0.498 6.283 15099 Z= 0.253 Chirality : 0.038 0.142 1808 Planarity : 0.003 0.039 1910 Dihedral : 7.821 145.808 1595 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1442 helix: 1.17 (0.18), residues: 876 sheet: -2.90 (0.51), residues: 79 loop : -1.75 (0.26), residues: 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 127 average time/residue: 2.2655 time to fit residues: 318.5376 Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.3497 time to fit residues: 4.5072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11111 Z= 0.198 Angle : 0.500 5.402 15099 Z= 0.255 Chirality : 0.038 0.144 1808 Planarity : 0.003 0.041 1910 Dihedral : 7.636 142.413 1595 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1442 helix: 1.23 (0.18), residues: 876 sheet: -2.81 (0.52), residues: 79 loop : -1.67 (0.26), residues: 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 2.2595 time to fit residues: 313.1662 Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.8743 time to fit residues: 5.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 11111 Z= 0.248 Angle : 0.514 5.465 15099 Z= 0.263 Chirality : 0.038 0.143 1808 Planarity : 0.003 0.051 1910 Dihedral : 7.591 138.218 1595 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1442 helix: 1.19 (0.18), residues: 877 sheet: -2.76 (0.52), residues: 79 loop : -1.66 (0.26), residues: 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 128 average time/residue: 2.1852 time to fit residues: 310.8679 Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 2.290 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.4023 time to fit residues: 2.8542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 11111 Z= 0.278 Angle : 0.531 5.839 15099 Z= 0.272 Chirality : 0.039 0.144 1808 Planarity : 0.004 0.056 1910 Dihedral : 7.573 133.065 1595 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1442 helix: 1.15 (0.18), residues: 875 sheet: -2.72 (0.52), residues: 79 loop : -1.69 (0.26), residues: 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 121 average time/residue: 2.3350 time to fit residues: 311.3357 Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.3857 time to fit residues: 3.3702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 11111 Z= 0.169 Angle : 0.497 5.442 15099 Z= 0.252 Chirality : 0.038 0.143 1808 Planarity : 0.003 0.050 1910 Dihedral : 7.259 122.388 1595 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1442 helix: 1.32 (0.18), residues: 876 sheet: -2.62 (0.53), residues: 79 loop : -1.57 (0.26), residues: 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 124 average time/residue: 2.2961 time to fit residues: 315.0675 Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.4152 time to fit residues: 2.8361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11111 Z= 0.193 Angle : 0.505 5.453 15099 Z= 0.257 Chirality : 0.038 0.143 1808 Planarity : 0.003 0.044 1910 Dihedral : 7.016 102.940 1595 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1442 helix: 1.38 (0.18), residues: 875 sheet: -2.57 (0.54), residues: 79 loop : -1.58 (0.26), residues: 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 127 average time/residue: 2.2602 time to fit residues: 319.4719 Evaluate side-chains 124 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.7444 time to fit residues: 3.9979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.085304 restraints weight = 42312.656| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.79 r_work: 0.2878 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11111 Z= 0.213 Angle : 0.509 5.460 15099 Z= 0.259 Chirality : 0.038 0.144 1808 Planarity : 0.003 0.043 1910 Dihedral : 6.699 67.684 1595 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1442 helix: 1.39 (0.18), residues: 872 sheet: -2.59 (0.54), residues: 79 loop : -1.59 (0.26), residues: 491 =============================================================================== Job complete usr+sys time: 6722.43 seconds wall clock time: 118 minutes 56.19 seconds (7136.19 seconds total)