Starting phenix.real_space_refine on Sun Feb 18 13:56:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/02_2024/7bgy_12184_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/02_2024/7bgy_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_12184/02_2024/7bgy_12184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/02_2024/7bgy_12184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/02_2024/7bgy_12184_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bgy_12184/02_2024/7bgy_12184_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.76, per 1000 atoms: 0.49 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: 21.68 Conformation dependent library (CDL) restraints added in 2.6 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: 4.26 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: 8.83 Time building geometry restraints manager: 22.02 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 - 28.70: 9920 28.70 - 57.40: 484 57.40 - 86.10: 50 86.10 - 114.81: 3 114.81 - 143.51: 3 Dihedral angle restraints: 10460 sinusoidal: 5779 harmonic: 4681 Sorted by residual: dihedral pdb=" C3 PEV A 801 " pdb=" C1 PEV A 801 " pdb=" C2 PEV A 801 " pdb=" O3P PEV A 801 " ideal model delta sinusoidal sigma weight residual 292.80 149.29 143.51 1 3.00e+01 1.11e-03 1.92e+01 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 ... (remaining 10457 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: 1.710 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: 0.330 Extract box with map and model: 8.200 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 82.010 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 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:14.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.040 ------------------------------------------------------------------------------- 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 : 14.148 143.508 3998 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 % Allowed : 7.14 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 73 HIS 0.006 0.001 HIS A 451 PHE 0.026 0.003 PHE A 109 TYR 0.027 0.003 TYR A 381 ARG 0.016 0.001 ARG A 21 *********************** 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 : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8235 (mmt) cc_final: 0.7634 (mmt) REVERT: A 112 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8449 (t0) REVERT: A 211 GLN cc_start: 0.8227 (mm110) cc_final: 0.7987 (mm-40) REVERT: A 316 SER cc_start: 0.8481 (m) cc_final: 0.8097 (p) REVERT: B 300 ASP cc_start: 0.6710 (m-30) cc_final: 0.6407 (m-30) REVERT: B 383 MET cc_start: 0.8265 (ptp) cc_final: 0.7884 (ptm) REVERT: B 515 MET cc_start: 0.8747 (ttt) cc_final: 0.8545 (ttt) outliers start: 5 outliers final: 2 residues processed: 156 average time/residue: 2.1600 time to fit residues: 373.0170 Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 628 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11111 Z= 0.223 Angle : 0.572 5.783 15099 Z= 0.295 Chirality : 0.039 0.148 1808 Planarity : 0.004 0.042 1910 Dihedral : 10.563 148.303 1621 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.32 % Allowed : 10.66 % Favored : 88.02 % 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: -3.50 (0.46), residues: 80 loop : -2.49 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 240 HIS 0.003 0.001 HIS A 451 PHE 0.011 0.001 PHE A 109 TYR 0.021 0.002 TYR A 381 ARG 0.004 0.000 ARG A 48 *********************** 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 142 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8367 (m) cc_final: 0.8033 (p) REVERT: A 366 MET cc_start: 0.8123 (mtp) cc_final: 0.7910 (mtp) REVERT: B 186 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7292 (p90) REVERT: B 383 MET cc_start: 0.8298 (ptp) cc_final: 0.7937 (ptm) outliers start: 15 outliers final: 6 residues processed: 136 average time/residue: 2.2020 time to fit residues: 331.2962 Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain C residue 68 ARG 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: 1.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN ** 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: 0.8000 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11111 Z= 0.275 Angle : 0.550 5.598 15099 Z= 0.286 Chirality : 0.039 0.147 1808 Planarity : 0.004 0.038 1910 Dihedral : 10.036 146.183 1617 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.41 % Allowed : 11.63 % Favored : 86.96 % 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: -0.91 (0.21), residues: 1442 helix: 0.58 (0.17), residues: 868 sheet: -3.28 (0.48), residues: 80 loop : -2.25 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 240 HIS 0.004 0.001 HIS A 451 PHE 0.012 0.001 PHE A 109 TYR 0.023 0.002 TYR A 381 ARG 0.005 0.000 ARG A 48 *********************** 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 135 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8386 (m) cc_final: 0.8072 (p) REVERT: A 366 MET cc_start: 0.8139 (mtp) cc_final: 0.7889 (mtp) REVERT: B 186 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.7375 (p90) REVERT: B 383 MET cc_start: 0.8248 (ptp) cc_final: 0.7882 (ptm) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 2.0882 time to fit residues: 301.9297 Evaluate side-chains 127 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 189 ASP 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: 0.4980 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 0.0050 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11111 Z= 0.160 Angle : 0.498 5.478 15099 Z= 0.255 Chirality : 0.038 0.141 1808 Planarity : 0.004 0.039 1910 Dihedral : 9.523 147.960 1617 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.06 % Allowed : 12.42 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1442 helix: 0.96 (0.18), residues: 871 sheet: -2.97 (0.51), residues: 80 loop : -1.89 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.002 0.000 HIS A 85 PHE 0.009 0.001 PHE A 494 TYR 0.021 0.001 TYR A 381 ARG 0.005 0.000 ARG A 48 *********************** 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 133 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 17 MET cc_start: 0.8029 (mmt) cc_final: 0.7537 (mmt) REVERT: A 316 SER cc_start: 0.8244 (m) cc_final: 0.8018 (p) REVERT: B 186 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7357 (p90) REVERT: B 383 MET cc_start: 0.8180 (ptp) cc_final: 0.7879 (ptm) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 2.1826 time to fit residues: 306.5167 Evaluate side-chains 126 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain C residue 68 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.0170 chunk 34 optimal weight: 1.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.1600 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= 0.254 Angle : 0.522 5.645 15099 Z= 0.269 Chirality : 0.039 0.143 1808 Planarity : 0.004 0.044 1910 Dihedral : 9.475 148.478 1617 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.15 % Allowed : 12.51 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1442 helix: 1.01 (0.18), residues: 871 sheet: -2.91 (0.51), residues: 79 loop : -1.83 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.004 0.001 HIS A 451 PHE 0.012 0.001 PHE A 109 TYR 0.022 0.001 TYR A 381 ARG 0.005 0.000 ARG A 48 *********************** 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 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8334 (m) cc_final: 0.8090 (p) REVERT: B 186 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.7326 (p90) REVERT: B 383 MET cc_start: 0.8202 (ptp) cc_final: 0.7904 (ptm) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 2.1748 time to fit residues: 298.4107 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 68 ARG 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: 0.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.1709 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= 0.219 Angle : 0.506 5.342 15099 Z= 0.261 Chirality : 0.038 0.143 1808 Planarity : 0.004 0.049 1910 Dihedral : 9.331 147.476 1617 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.15 % Allowed : 12.86 % Favored : 85.99 % 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: -0.14 (0.22), residues: 1442 helix: 1.06 (0.18), residues: 876 sheet: -2.80 (0.52), residues: 79 loop : -1.73 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 240 HIS 0.003 0.000 HIS A 85 PHE 0.010 0.001 PHE A 109 TYR 0.021 0.001 TYR A 381 ARG 0.006 0.000 ARG A 48 *********************** 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 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8285 (m) cc_final: 0.8066 (p) REVERT: B 186 TRP cc_start: 0.8340 (OUTLIER) cc_final: 0.7332 (p90) REVERT: B 383 MET cc_start: 0.8235 (ptp) cc_final: 0.7957 (ptm) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 2.1667 time to fit residues: 297.7933 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 68 ARG 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: 0.1980 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 85 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1774 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= 0.214 Angle : 0.503 5.360 15099 Z= 0.259 Chirality : 0.038 0.143 1808 Planarity : 0.004 0.046 1910 Dihedral : 9.207 145.289 1617 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.23 % Allowed : 13.13 % Favored : 85.64 % 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: -0.04 (0.22), residues: 1442 helix: 1.12 (0.18), residues: 876 sheet: -2.73 (0.53), residues: 79 loop : -1.67 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.003 0.000 HIS A 85 PHE 0.019 0.001 PHE B 322 TYR 0.021 0.001 TYR A 381 ARG 0.005 0.000 ARG A 48 *********************** 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 135 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8347 (m) cc_final: 0.8136 (p) REVERT: B 186 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.7343 (p90) REVERT: B 383 MET cc_start: 0.8240 (ptp) cc_final: 0.7959 (ptm) outliers start: 14 outliers final: 12 residues processed: 127 average time/residue: 2.0943 time to fit residues: 295.9838 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 68 ARG 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: 0.0570 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 108 optimal weight: 0.0570 chunk 125 optimal weight: 0.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11111 Z= 0.150 Angle : 0.483 6.342 15099 Z= 0.246 Chirality : 0.037 0.142 1808 Planarity : 0.004 0.044 1910 Dihedral : 8.886 142.576 1617 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.06 % Allowed : 13.66 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1442 helix: 1.34 (0.18), residues: 875 sheet: -2.66 (0.54), residues: 79 loop : -1.55 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.002 0.000 HIS A 85 PHE 0.014 0.001 PHE B 322 TYR 0.021 0.001 TYR A 381 ARG 0.005 0.000 ARG A 48 *********************** 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 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.7296 (p90) REVERT: B 316 ASN cc_start: 0.7613 (m-40) cc_final: 0.6826 (m-40) REVERT: B 383 MET cc_start: 0.8225 (ptp) cc_final: 0.7940 (ptm) outliers start: 12 outliers final: 9 residues processed: 124 average time/residue: 2.2553 time to fit residues: 308.8214 Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain C residue 68 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.1909 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= 0.258 Angle : 0.514 5.502 15099 Z= 0.265 Chirality : 0.039 0.144 1808 Planarity : 0.004 0.048 1910 Dihedral : 8.888 139.974 1617 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.32 % Allowed : 13.92 % Favored : 84.76 % 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: 0.11 (0.22), residues: 1442 helix: 1.26 (0.18), residues: 873 sheet: -2.67 (0.54), residues: 79 loop : -1.62 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.004 0.001 HIS A 451 PHE 0.012 0.001 PHE A 109 TYR 0.021 0.001 TYR A 381 ARG 0.004 0.000 ARG A 48 *********************** 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 132 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TRP cc_start: 0.8312 (OUTLIER) cc_final: 0.7297 (p90) REVERT: B 383 MET cc_start: 0.8255 (ptp) cc_final: 0.7977 (ptm) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 2.2179 time to fit residues: 306.6214 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain C residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7980 moved from start: 0.1951 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= 0.229 Angle : 0.507 5.470 15099 Z= 0.261 Chirality : 0.038 0.144 1808 Planarity : 0.004 0.047 1910 Dihedral : 8.693 139.298 1617 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.97 % Allowed : 14.27 % Favored : 84.76 % 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: 0.13 (0.22), residues: 1442 helix: 1.27 (0.18), residues: 873 sheet: -2.63 (0.54), residues: 79 loop : -1.61 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 240 HIS 0.003 0.000 HIS A 85 PHE 0.016 0.001 PHE A 392 TYR 0.021 0.001 TYR A 381 ARG 0.004 0.000 ARG A 44 ********************** 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 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 TRP cc_start: 0.8302 (OUTLIER) cc_final: 0.7312 (p90) REVERT: B 383 MET cc_start: 0.8256 (ptp) cc_final: 0.7977 (ptm) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 2.2004 time to fit residues: 287.4713 Evaluate side-chains 124 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain C residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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** ** B 653 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 = 0.3414 r_free = 0.3414 target = 0.114547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.086572 restraints weight = 43149.094| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.87 r_work: 0.2910 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11111 Z= 0.157 Angle : 0.485 5.518 15099 Z= 0.247 Chirality : 0.037 0.143 1808 Planarity : 0.003 0.046 1910 Dihedral : 8.043 138.300 1617 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.88 % Allowed : 14.36 % Favored : 84.76 % 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: 0.36 (0.22), residues: 1442 helix: 1.45 (0.18), residues: 875 sheet: -2.55 (0.55), residues: 79 loop : -1.50 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 240 HIS 0.002 0.000 HIS A 85 PHE 0.008 0.001 PHE A 494 TYR 0.021 0.001 TYR A 381 ARG 0.004 0.000 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7041.27 seconds wall clock time: 124 minutes 11.07 seconds (7451.07 seconds total)