Starting phenix.real_space_refine on Mon Mar 11 11:13:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/03_2024/7uxa_26856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/03_2024/7uxa_26856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/03_2024/7uxa_26856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/03_2024/7uxa_26856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/03_2024/7uxa_26856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/03_2024/7uxa_26856.pdb" } resolution = 3.28 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= 0.052 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: 6 Type Number sf(0) Gaussians P 77 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 4890 2.51 5 N 1420 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1762 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 117} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1615 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2105 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1667 Unusual residues: {' MG': 2} Inner-chain residues flagged as termini: ['pdbres=" A E 47 "'] Classifications: {'RNA': 78, 'undetermined': 2} Modifications used: {'5*END': 1, 'p5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 64, None: 2} Not linked: pdbres=" G E 88 " pdbres=" MG E 101 " Not linked: pdbres=" MG E 101 " pdbres=" MG E 102 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.28, per 1000 atoms: 0.65 Number of scatterers: 8120 At special positions: 0 Unit cell: (87.608, 86.676, 123.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 77 15.00 Mg 2 11.99 O 1705 8.00 N 1420 7.00 C 4890 6.00 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 35.4% alpha, 16.3% beta 27 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 83 through 101 removed outlier: 3.593A pdb=" N GLN A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.608A pdb=" N ASP A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'B' and resid 44 through 53 removed outlier: 4.314A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 53 " --> pdb=" O MET B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 73 Processing helix chain 'B' and resid 116 through 131 Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 430 through 443 removed outlier: 3.824A pdb=" N GLU C 435 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Proline residue: C 437 - end of helix removed outlier: 3.622A pdb=" N ILE C 443 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 27 removed outlier: 3.851A pdb=" N ARG D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 67 removed outlier: 3.707A pdb=" N ALA D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.611A pdb=" N THR D 101 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.673A pdb=" N LEU D 145 " --> pdb=" O TYR D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.842A pdb=" N ALA D 459 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.512A pdb=" N SER A 11 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 2 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 69 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL A 4 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.524A pdb=" N GLU D 72 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG D 70 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 235 removed outlier: 4.610A pdb=" N LEU A 289 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 291 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 235 removed outlier: 4.610A pdb=" N LEU A 289 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 291 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 288 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 302 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 104 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA B 142 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 106 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL B 144 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 108 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE B 90 " --> pdb=" O PRO B 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 269 removed outlier: 4.115A pdb=" N LEU B 114 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 297 through 299 removed outlier: 3.850A pdb=" N VAL C 49 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE C 40 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR C 317 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA C 42 " --> pdb=" O TYR C 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.025A pdb=" N TYR C 380 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 387 removed outlier: 3.540A pdb=" N LEU C 423 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU C 447 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS D 474 " --> pdb=" O ALA D 503 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL D 505 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER D 476 " --> pdb=" O VAL D 505 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 104 through 106 264 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2137 1.33 - 1.45: 1945 1.45 - 1.57: 4193 1.57 - 1.69: 153 1.69 - 1.81: 41 Bond restraints: 8469 Sorted by residual: bond pdb=" CA GLY B 94 " pdb=" C GLY B 94 " ideal model delta sigma weight residual 1.521 1.511 0.011 1.13e-02 7.83e+03 8.78e-01 bond pdb=" CB TRP D 99 " pdb=" CG TRP D 99 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.02e-01 bond pdb=" CA ALA A 286 " pdb=" C ALA A 286 " ideal model delta sigma weight residual 1.522 1.531 -0.009 1.08e-02 8.57e+03 6.87e-01 bond pdb=" CA ALA C 377 " pdb=" C ALA C 377 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.49e-01 bond pdb=" CA GLU C 458 " pdb=" C GLU C 458 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.10e-02 8.26e+03 6.09e-01 ... (remaining 8464 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 709 107.06 - 113.80: 4830 113.80 - 120.55: 3241 120.55 - 127.30: 2852 127.30 - 134.05: 237 Bond angle restraints: 11869 Sorted by residual: angle pdb=" N ASP A 243 " pdb=" CA ASP A 243 " pdb=" C ASP A 243 " ideal model delta sigma weight residual 114.75 111.06 3.69 1.26e+00 6.30e-01 8.60e+00 angle pdb=" N THR D 429 " pdb=" CA THR D 429 " pdb=" C THR D 429 " ideal model delta sigma weight residual 107.23 111.62 -4.39 1.67e+00 3.59e-01 6.92e+00 angle pdb=" N LYS C 371 " pdb=" CA LYS C 371 " pdb=" C LYS C 371 " ideal model delta sigma weight residual 108.19 111.38 -3.19 1.29e+00 6.01e-01 6.13e+00 angle pdb=" N TYR C 362 " pdb=" CA TYR C 362 " pdb=" C TYR C 362 " ideal model delta sigma weight residual 109.65 105.95 3.70 1.56e+00 4.11e-01 5.64e+00 angle pdb=" N VAL C 335 " pdb=" CA VAL C 335 " pdb=" C VAL C 335 " ideal model delta sigma weight residual 113.07 110.04 3.03 1.36e+00 5.41e-01 4.97e+00 ... (remaining 11864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 4821 24.49 - 48.98: 204 48.98 - 73.47: 139 73.47 - 97.97: 11 97.97 - 122.46: 3 Dihedral angle restraints: 5178 sinusoidal: 2805 harmonic: 2373 Sorted by residual: dihedral pdb=" CA LEU C 360 " pdb=" C LEU C 360 " pdb=" N LYS C 361 " pdb=" CA LYS C 361 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" O4' G E 72 " pdb=" C1' G E 72 " pdb=" N9 G E 72 " pdb=" C4 G E 72 " ideal model delta sinusoidal sigma weight residual -90.00 -19.43 -70.57 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" O4' A E 52 " pdb=" C1' A E 52 " pdb=" N9 A E 52 " pdb=" C4 A E 52 " ideal model delta sinusoidal sigma weight residual -106.00 -158.89 52.89 1 1.70e+01 3.46e-03 1.32e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1053 0.037 - 0.074: 249 0.074 - 0.111: 69 0.111 - 0.147: 12 0.147 - 0.184: 1 Chirality restraints: 1384 Sorted by residual: chirality pdb=" C1' A E 74 " pdb=" O4' A E 74 " pdb=" C2' A E 74 " pdb=" N9 A E 74 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" C1' G E 22 " pdb=" O4' G E 22 " pdb=" C2' G E 22 " pdb=" N9 G E 22 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1381 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 373 " -0.036 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO C 374 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 374 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 374 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A E 74 " 0.024 2.00e-02 2.50e+03 1.10e-02 3.32e+00 pdb=" N9 A E 74 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A E 74 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A E 74 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A E 74 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A E 74 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A E 74 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A E 74 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A E 74 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A E 74 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A E 74 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 6 " -0.020 2.00e-02 2.50e+03 1.08e-02 2.61e+00 pdb=" N1 U E 6 " 0.024 2.00e-02 2.50e+03 pdb=" C2 U E 6 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U E 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U E 6 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U E 6 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U E 6 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U E 6 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U E 6 " 0.003 2.00e-02 2.50e+03 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 142 2.65 - 3.21: 7217 3.21 - 3.77: 13257 3.77 - 4.34: 17916 4.34 - 4.90: 28118 Nonbonded interactions: 66650 Sorted by model distance: nonbonded pdb=" OP1 G E 9 " pdb="MG MG E 101 " model vdw 2.084 2.170 nonbonded pdb=" OG SER D 495 " pdb=" O VAL D 498 " model vdw 2.168 2.440 nonbonded pdb=" OE1 GLU A 62 " pdb=" OH TYR A 221 " model vdw 2.199 2.440 nonbonded pdb=" NH2 ARG D 27 " pdb=" OP1 G E 17 " model vdw 2.252 2.520 nonbonded pdb=" OE1 GLU D 122 " pdb=" OH TYR D 155 " model vdw 2.255 2.440 ... (remaining 66645 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.120 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.840 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.028 8469 Z= 0.221 Angle : 0.577 5.955 11869 Z= 0.330 Chirality : 0.036 0.184 1384 Planarity : 0.004 0.054 1229 Dihedral : 16.774 122.458 3648 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.88 % Allowed : 6.00 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.97 (0.31), residues: 805 helix: 0.29 (0.31), residues: 276 sheet: -1.95 (0.45), residues: 128 loop : -0.75 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.003 0.001 HIS A 211 PHE 0.013 0.001 PHE A 244 TYR 0.010 0.001 TYR D 155 ARG 0.003 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.7116 (mtp180) REVERT: B 59 GLN cc_start: 0.8097 (mt0) cc_final: 0.7868 (mp10) REVERT: B 81 CYS cc_start: 0.9034 (m) cc_final: 0.8592 (p) REVERT: B 147 ASP cc_start: 0.8943 (t0) cc_final: 0.8663 (t0) REVERT: B 161 LEU cc_start: 0.8177 (mt) cc_final: 0.7880 (pt) REVERT: C 46 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7287 (m-40) REVERT: C 58 GLU cc_start: 0.5999 (mt-10) cc_final: 0.4964 (tp30) REVERT: C 317 TYR cc_start: 0.6729 (m-80) cc_final: 0.6519 (m-80) REVERT: C 367 LEU cc_start: 0.8298 (mt) cc_final: 0.7883 (mp) REVERT: C 429 MET cc_start: 0.6062 (tmm) cc_final: 0.5803 (tmm) outliers start: 6 outliers final: 1 residues processed: 161 average time/residue: 0.2176 time to fit residues: 46.7333 Evaluate side-chains 106 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 447 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.0040 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.5732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8469 Z= 0.164 Angle : 0.503 5.660 11869 Z= 0.258 Chirality : 0.037 0.170 1384 Planarity : 0.004 0.049 1229 Dihedral : 18.873 117.659 2121 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.61 % Allowed : 11.42 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.43 (0.31), residues: 805 helix: 0.82 (0.32), residues: 272 sheet: -1.56 (0.46), residues: 126 loop : -0.53 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 99 HIS 0.002 0.001 HIS B 77 PHE 0.012 0.001 PHE A 86 TYR 0.016 0.001 TYR B 67 ARG 0.005 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7586 (mmt-90) cc_final: 0.7071 (mtp180) REVERT: B 161 LEU cc_start: 0.8156 (mt) cc_final: 0.7846 (pt) REVERT: C 44 MET cc_start: 0.8006 (tpp) cc_final: 0.7453 (tpt) REVERT: C 348 TYR cc_start: 0.7223 (t80) cc_final: 0.6916 (t80) REVERT: C 367 LEU cc_start: 0.8114 (mt) cc_final: 0.7694 (mp) REVERT: C 413 ASN cc_start: 0.8032 (m-40) cc_final: 0.7802 (m110) REVERT: D 90 GLU cc_start: 0.8408 (tt0) cc_final: 0.8108 (pt0) REVERT: D 460 THR cc_start: 0.9298 (p) cc_final: 0.8909 (t) REVERT: D 465 ASN cc_start: 0.8277 (p0) cc_final: 0.8031 (p0) REVERT: D 509 ASP cc_start: 0.8496 (t0) cc_final: 0.8236 (t70) outliers start: 11 outliers final: 5 residues processed: 119 average time/residue: 0.2329 time to fit residues: 36.7587 Evaluate side-chains 111 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 519 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 59 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8469 Z= 0.233 Angle : 0.530 5.526 11869 Z= 0.271 Chirality : 0.038 0.173 1384 Planarity : 0.004 0.050 1229 Dihedral : 18.705 114.795 2116 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.34 % Allowed : 12.30 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.30 (0.31), residues: 805 helix: 0.92 (0.31), residues: 272 sheet: -1.37 (0.45), residues: 134 loop : -0.47 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 63 HIS 0.002 0.001 HIS A 217 PHE 0.011 0.001 PHE A 244 TYR 0.018 0.002 TYR D 155 ARG 0.008 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.748 Fit side-chains REVERT: A 10 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7133 (mtp180) REVERT: A 205 GLN cc_start: 0.6705 (tm-30) cc_final: 0.6140 (tm-30) REVERT: B 59 GLN cc_start: 0.8198 (mp10) cc_final: 0.7972 (mp10) REVERT: B 71 MET cc_start: 0.8117 (tpt) cc_final: 0.7724 (tpt) REVERT: B 89 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 161 LEU cc_start: 0.8194 (mt) cc_final: 0.7842 (pt) REVERT: C 44 MET cc_start: 0.7708 (tpp) cc_final: 0.7463 (tpt) REVERT: C 68 LYS cc_start: 0.6618 (tttt) cc_final: 0.6294 (ttpp) REVERT: C 348 TYR cc_start: 0.7553 (t80) cc_final: 0.6999 (t80) REVERT: C 419 MET cc_start: 0.7980 (mtt) cc_final: 0.7486 (mtt) REVERT: D 90 GLU cc_start: 0.8461 (tt0) cc_final: 0.8051 (pm20) REVERT: D 460 THR cc_start: 0.9296 (p) cc_final: 0.8915 (t) REVERT: D 465 ASN cc_start: 0.8558 (p0) cc_final: 0.8276 (p0) REVERT: D 520 LEU cc_start: 0.7707 (mm) cc_final: 0.7492 (mm) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.1918 time to fit residues: 31.6807 Evaluate side-chains 108 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 71 optimal weight: 0.1980 chunk 48 optimal weight: 6.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 43 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8469 Z= 0.132 Angle : 0.477 5.857 11869 Z= 0.245 Chirality : 0.036 0.180 1384 Planarity : 0.004 0.048 1229 Dihedral : 18.664 113.885 2116 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.61 % Allowed : 14.06 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.02 (0.31), residues: 805 helix: 1.20 (0.32), residues: 272 sheet: -1.07 (0.46), residues: 134 loop : -0.33 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 63 HIS 0.002 0.000 HIS A 217 PHE 0.012 0.001 PHE A 233 TYR 0.012 0.001 TYR D 470 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7596 (mmt-90) cc_final: 0.7178 (mtp180) REVERT: A 205 GLN cc_start: 0.6670 (tm-30) cc_final: 0.6135 (tm-30) REVERT: B 59 GLN cc_start: 0.8281 (mp10) cc_final: 0.7874 (mp10) REVERT: B 132 ASP cc_start: 0.8165 (t70) cc_final: 0.7897 (t0) REVERT: B 161 LEU cc_start: 0.8157 (mt) cc_final: 0.7795 (pt) REVERT: C 44 MET cc_start: 0.8010 (tpp) cc_final: 0.7438 (tpt) REVERT: C 47 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6938 (p0) REVERT: C 68 LYS cc_start: 0.6319 (tttt) cc_final: 0.6066 (ttpp) REVERT: C 348 TYR cc_start: 0.7472 (t80) cc_final: 0.6902 (t80) REVERT: C 364 THR cc_start: 0.9104 (p) cc_final: 0.8903 (p) REVERT: D 63 TRP cc_start: 0.8518 (m100) cc_final: 0.8307 (m100) REVERT: D 90 GLU cc_start: 0.8373 (tt0) cc_final: 0.8044 (pm20) REVERT: D 460 THR cc_start: 0.9216 (p) cc_final: 0.8875 (t) REVERT: D 465 ASN cc_start: 0.8521 (p0) cc_final: 0.8198 (p0) REVERT: D 509 ASP cc_start: 0.8393 (t0) cc_final: 0.8159 (t70) outliers start: 11 outliers final: 6 residues processed: 115 average time/residue: 0.1884 time to fit residues: 30.2827 Evaluate side-chains 106 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 78 HIS ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8469 Z= 0.289 Angle : 0.540 6.406 11869 Z= 0.275 Chirality : 0.038 0.178 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.649 112.664 2116 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.49 % Allowed : 14.79 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.31), residues: 805 helix: 0.97 (0.31), residues: 277 sheet: -1.48 (0.44), residues: 146 loop : -0.40 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 82 HIS 0.002 0.001 HIS A 211 PHE 0.011 0.002 PHE A 244 TYR 0.022 0.002 TYR D 155 ARG 0.011 0.001 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7649 (mmt-90) cc_final: 0.7172 (mtp180) REVERT: A 94 PHE cc_start: 0.8059 (t80) cc_final: 0.7774 (t80) REVERT: B 40 MET cc_start: 0.6363 (mtp) cc_final: 0.6092 (mtp) REVERT: B 59 GLN cc_start: 0.8368 (mp10) cc_final: 0.7883 (mp10) REVERT: B 124 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8409 (mmtp) REVERT: B 161 LEU cc_start: 0.8162 (mt) cc_final: 0.7822 (pt) REVERT: C 44 MET cc_start: 0.7852 (tpp) cc_final: 0.7629 (tpt) REVERT: C 348 TYR cc_start: 0.7952 (t80) cc_final: 0.7313 (t80) REVERT: D 63 TRP cc_start: 0.8623 (m100) cc_final: 0.8395 (m100) REVERT: D 90 GLU cc_start: 0.8481 (tt0) cc_final: 0.8078 (pm20) REVERT: D 460 THR cc_start: 0.9252 (p) cc_final: 0.8912 (t) REVERT: D 465 ASN cc_start: 0.8627 (p0) cc_final: 0.8279 (p0) outliers start: 17 outliers final: 12 residues processed: 110 average time/residue: 0.1721 time to fit residues: 27.3143 Evaluate side-chains 108 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8469 Z= 0.215 Angle : 0.506 5.912 11869 Z= 0.256 Chirality : 0.037 0.186 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.655 112.069 2116 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.34 % Allowed : 15.67 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -0.08 (0.31), residues: 805 helix: 1.09 (0.31), residues: 277 sheet: -0.98 (0.46), residues: 134 loop : -0.46 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 354 HIS 0.002 0.001 HIS A 211 PHE 0.012 0.001 PHE A 233 TYR 0.015 0.001 TYR D 155 ARG 0.008 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7632 (mmt-90) cc_final: 0.7178 (mtp180) REVERT: A 94 PHE cc_start: 0.8011 (t80) cc_final: 0.7763 (t80) REVERT: B 40 MET cc_start: 0.6368 (mtp) cc_final: 0.5801 (mtp) REVERT: B 59 GLN cc_start: 0.8373 (mp10) cc_final: 0.7921 (mp10) REVERT: B 65 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8063 (tt) REVERT: B 88 GLN cc_start: 0.8759 (pp30) cc_final: 0.8520 (pp30) REVERT: B 124 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8437 (mmtp) REVERT: B 161 LEU cc_start: 0.8118 (mt) cc_final: 0.7727 (pt) REVERT: C 44 MET cc_start: 0.7827 (tpp) cc_final: 0.7513 (tpt) REVERT: C 47 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6762 (p0) REVERT: C 340 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7532 (mmm-85) REVERT: C 348 TYR cc_start: 0.7899 (t80) cc_final: 0.7252 (t80) REVERT: D 63 TRP cc_start: 0.8597 (m100) cc_final: 0.8353 (m100) REVERT: D 90 GLU cc_start: 0.8446 (tt0) cc_final: 0.8118 (pm20) REVERT: D 460 THR cc_start: 0.9213 (p) cc_final: 0.8903 (t) REVERT: D 465 ASN cc_start: 0.8604 (p0) cc_final: 0.8232 (p0) REVERT: D 478 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8666 (t80) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 0.1817 time to fit residues: 28.3043 Evaluate side-chains 111 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 478 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8469 Z= 0.175 Angle : 0.485 5.822 11869 Z= 0.246 Chirality : 0.036 0.184 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.635 111.065 2116 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.20 % Allowed : 16.84 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.31), residues: 805 helix: 1.20 (0.32), residues: 277 sheet: -0.84 (0.47), residues: 134 loop : -0.42 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 99 HIS 0.002 0.001 HIS A 211 PHE 0.013 0.001 PHE A 233 TYR 0.013 0.001 TYR D 155 ARG 0.007 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7636 (mmt-90) cc_final: 0.7197 (mtp180) REVERT: A 205 GLN cc_start: 0.6686 (tm-30) cc_final: 0.6185 (tm-30) REVERT: B 40 MET cc_start: 0.6238 (mtp) cc_final: 0.5799 (mtp) REVERT: B 59 GLN cc_start: 0.8294 (mp10) cc_final: 0.7796 (mp10) REVERT: B 65 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8020 (tt) REVERT: B 124 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8455 (mmtp) REVERT: B 152 TYR cc_start: 0.8221 (m-80) cc_final: 0.7985 (m-80) REVERT: B 161 LEU cc_start: 0.8147 (mt) cc_final: 0.7767 (pt) REVERT: C 44 MET cc_start: 0.7889 (tpp) cc_final: 0.7584 (tpt) REVERT: C 47 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6753 (p0) REVERT: C 340 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: C 348 TYR cc_start: 0.7914 (t80) cc_final: 0.7281 (t80) REVERT: D 63 TRP cc_start: 0.8595 (m100) cc_final: 0.8302 (m100) REVERT: D 90 GLU cc_start: 0.8403 (tt0) cc_final: 0.8095 (pm20) REVERT: D 460 THR cc_start: 0.9180 (p) cc_final: 0.8880 (t) REVERT: D 465 ASN cc_start: 0.8599 (p0) cc_final: 0.8219 (p0) outliers start: 15 outliers final: 9 residues processed: 110 average time/residue: 0.1919 time to fit residues: 29.5984 Evaluate side-chains 109 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 150 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8469 Z= 0.153 Angle : 0.476 5.877 11869 Z= 0.242 Chirality : 0.036 0.184 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.604 109.662 2116 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.05 % Allowed : 17.13 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.09 (0.31), residues: 805 helix: 1.25 (0.32), residues: 279 sheet: -0.71 (0.47), residues: 134 loop : -0.45 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 99 HIS 0.002 0.000 HIS A 217 PHE 0.013 0.001 PHE A 233 TYR 0.015 0.001 TYR D 470 ARG 0.006 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7631 (mmt-90) cc_final: 0.7218 (mtp180) REVERT: A 205 GLN cc_start: 0.6674 (tm-30) cc_final: 0.6134 (tm-30) REVERT: B 40 MET cc_start: 0.6222 (mtp) cc_final: 0.5806 (mtp) REVERT: B 59 GLN cc_start: 0.8265 (mp10) cc_final: 0.7759 (mp10) REVERT: B 65 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8053 (tt) REVERT: B 124 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8468 (mmtp) REVERT: B 152 TYR cc_start: 0.8167 (m-80) cc_final: 0.7432 (m-80) REVERT: B 161 LEU cc_start: 0.8132 (mt) cc_final: 0.7776 (pt) REVERT: C 44 MET cc_start: 0.7880 (tpp) cc_final: 0.7509 (tpt) REVERT: C 340 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7560 (mmm-85) REVERT: C 348 TYR cc_start: 0.7908 (t80) cc_final: 0.7256 (t80) REVERT: D 63 TRP cc_start: 0.8591 (m100) cc_final: 0.8270 (m100) REVERT: D 90 GLU cc_start: 0.8416 (tt0) cc_final: 0.8086 (pm20) REVERT: D 460 THR cc_start: 0.9146 (p) cc_final: 0.8866 (t) REVERT: D 465 ASN cc_start: 0.8584 (p0) cc_final: 0.8199 (p0) REVERT: D 478 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8613 (t80) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.1835 time to fit residues: 27.5775 Evaluate side-chains 105 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 478 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8469 Z= 0.221 Angle : 0.511 7.315 11869 Z= 0.260 Chirality : 0.037 0.181 1384 Planarity : 0.004 0.047 1229 Dihedral : 18.592 109.237 2116 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.34 % Allowed : 16.98 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.31), residues: 805 helix: 1.19 (0.31), residues: 279 sheet: -0.71 (0.47), residues: 134 loop : -0.49 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 99 HIS 0.002 0.000 HIS A 211 PHE 0.014 0.001 PHE A 233 TYR 0.014 0.001 TYR D 470 ARG 0.006 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7197 (mtp180) REVERT: A 205 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6193 (tm-30) REVERT: B 40 MET cc_start: 0.6321 (mtp) cc_final: 0.5898 (mtp) REVERT: B 59 GLN cc_start: 0.8311 (mp10) cc_final: 0.7834 (mp10) REVERT: B 65 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 124 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8477 (mmtp) REVERT: B 152 TYR cc_start: 0.8237 (m-80) cc_final: 0.8002 (m-80) REVERT: B 161 LEU cc_start: 0.8138 (mt) cc_final: 0.7751 (pt) REVERT: C 44 MET cc_start: 0.7886 (tpp) cc_final: 0.7514 (tpt) REVERT: C 340 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7630 (mmm-85) REVERT: C 348 TYR cc_start: 0.7974 (t80) cc_final: 0.7333 (t80) REVERT: D 63 TRP cc_start: 0.8607 (m100) cc_final: 0.8333 (m100) REVERT: D 90 GLU cc_start: 0.8422 (tt0) cc_final: 0.8125 (pm20) REVERT: D 460 THR cc_start: 0.9165 (p) cc_final: 0.8875 (t) REVERT: D 465 ASN cc_start: 0.8618 (p0) cc_final: 0.8226 (p0) REVERT: D 478 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8658 (t80) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.1948 time to fit residues: 29.0492 Evaluate side-chains 105 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 478 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 21 optimal weight: 0.0060 chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN C 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8469 Z= 0.143 Angle : 0.482 7.106 11869 Z= 0.245 Chirality : 0.036 0.185 1384 Planarity : 0.004 0.049 1229 Dihedral : 18.571 107.889 2116 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.05 % Allowed : 17.13 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.31), residues: 805 helix: 1.47 (0.32), residues: 274 sheet: -0.52 (0.48), residues: 132 loop : -0.31 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 99 HIS 0.002 0.001 HIS A 217 PHE 0.014 0.001 PHE A 233 TYR 0.014 0.001 TYR D 470 ARG 0.009 0.000 ARG C 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7225 (mtp180) REVERT: A 205 GLN cc_start: 0.6708 (tm-30) cc_final: 0.6220 (tm-30) REVERT: B 40 MET cc_start: 0.6292 (mtp) cc_final: 0.5847 (mtp) REVERT: B 59 GLN cc_start: 0.8271 (mp10) cc_final: 0.7839 (mp10) REVERT: B 65 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8048 (tt) REVERT: B 124 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8474 (mmtp) REVERT: B 132 ASP cc_start: 0.8139 (t0) cc_final: 0.7580 (t0) REVERT: B 152 TYR cc_start: 0.8140 (m-80) cc_final: 0.7411 (m-80) REVERT: B 161 LEU cc_start: 0.8094 (mt) cc_final: 0.7783 (pt) REVERT: C 44 MET cc_start: 0.7877 (tpp) cc_final: 0.7503 (tpt) REVERT: C 348 TYR cc_start: 0.7922 (t80) cc_final: 0.7305 (t80) REVERT: C 442 ARG cc_start: 0.8587 (ttm110) cc_final: 0.8364 (mtp-110) REVERT: D 63 TRP cc_start: 0.8587 (m100) cc_final: 0.8296 (m100) REVERT: D 90 GLU cc_start: 0.8389 (tt0) cc_final: 0.8063 (pm20) REVERT: D 460 THR cc_start: 0.9102 (p) cc_final: 0.8857 (t) REVERT: D 465 ASN cc_start: 0.8585 (p0) cc_final: 0.8195 (p0) REVERT: D 478 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8639 (t80) REVERT: D 509 ASP cc_start: 0.8429 (t0) cc_final: 0.8196 (t70) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.1974 time to fit residues: 28.0626 Evaluate side-chains 102 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 478 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.0050 chunk 62 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.160106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123775 restraints weight = 12362.059| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.41 r_work: 0.3497 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 8469 Z= 0.159 Angle : 0.840 59.178 11869 Z= 0.477 Chirality : 0.037 0.312 1384 Planarity : 0.004 0.046 1229 Dihedral : 18.571 107.866 2116 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.10 % Favored : 95.78 % Rotamer: Outliers : 2.20 % Allowed : 17.13 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.35 (0.31), residues: 805 helix: 1.48 (0.32), residues: 274 sheet: -0.49 (0.48), residues: 132 loop : -0.33 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 99 HIS 0.002 0.001 HIS A 217 PHE 0.012 0.001 PHE A 233 TYR 0.012 0.001 TYR D 470 ARG 0.007 0.000 ARG C 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1906.79 seconds wall clock time: 35 minutes 18.68 seconds (2118.68 seconds total)