Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 13:10:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/08_2023/7uxa_26856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/08_2023/7uxa_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_26856/08_2023/7uxa_26856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/08_2023/7uxa_26856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/08_2023/7uxa_26856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxa_26856/08_2023/7uxa_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 4.91, per 1000 atoms: 0.60 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: 3.69 Conformation dependent library (CDL) restraints added in 1.1 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: 2.78 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: 2.58 Time building geometry restraints manager: 3.91 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: 4722 24.49 - 48.98: 135 48.98 - 73.47: 25 73.47 - 97.97: 5 97.97 - 122.46: 3 Dihedral angle restraints: 4890 sinusoidal: 2517 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 4887 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: 1.950 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: 7.540 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.100 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- 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 : 11.946 122.458 3360 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 % 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 *********************** 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 : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 161 average time/residue: 0.2138 time to fit residues: 45.9529 Evaluate side-chains 103 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1058 time to fit residues: 1.1893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.1854 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= 0.235 Angle : 0.548 6.121 11869 Z= 0.280 Chirality : 0.038 0.176 1384 Planarity : 0.004 0.050 1229 Dihedral : 11.233 120.853 1828 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.90 % 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: -0.66 (0.31), residues: 805 helix: 0.57 (0.32), residues: 278 sheet: -1.67 (0.45), residues: 128 loop : -0.63 (0.34), residues: 399 *********************** 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 128 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.819 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 123 average time/residue: 0.2209 time to fit residues: 36.4654 Evaluate side-chains 106 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0705 time to fit residues: 2.1983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 59 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN D 35 GLN D 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2330 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= 0.212 Angle : 0.521 5.854 11869 Z= 0.265 Chirality : 0.037 0.182 1384 Planarity : 0.004 0.050 1229 Dihedral : 11.129 118.699 1828 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 1.17 % 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: 0.90 (0.31), residues: 272 sheet: -1.36 (0.45), residues: 134 loop : -0.45 (0.34), residues: 399 *********************** 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 110 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.769 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 106 average time/residue: 0.1874 time to fit residues: 27.8224 Evaluate side-chains 91 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 413 ASN 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: 0.8167 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 8469 Z= 0.348 Angle : 0.605 5.803 11869 Z= 0.309 Chirality : 0.040 0.183 1384 Planarity : 0.004 0.050 1229 Dihedral : 11.371 117.531 1828 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 1.76 % 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: -0.48 (0.31), residues: 805 helix: 0.73 (0.31), residues: 270 sheet: -1.73 (0.43), residues: 146 loop : -0.37 (0.35), residues: 389 *********************** 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 113 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.1812 time to fit residues: 26.8803 Evaluate side-chains 105 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0770 time to fit residues: 2.1779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8469 Z= 0.267 Angle : 0.549 5.579 11869 Z= 0.280 Chirality : 0.038 0.190 1384 Planarity : 0.004 0.050 1229 Dihedral : 11.293 116.642 1828 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 1.32 % 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: -0.32 (0.31), residues: 805 helix: 0.85 (0.31), residues: 272 sheet: -1.26 (0.45), residues: 134 loop : -0.48 (0.35), residues: 399 *********************** 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 112 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 109 average time/residue: 0.1698 time to fit residues: 27.0165 Evaluate side-chains 102 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0774 time to fit residues: 1.2908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2891 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= 0.183 Angle : 0.517 8.553 11869 Z= 0.260 Chirality : 0.037 0.192 1384 Planarity : 0.004 0.049 1229 Dihedral : 11.111 114.399 1828 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 1.17 % 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: -0.15 (0.31), residues: 805 helix: 1.03 (0.31), residues: 272 sheet: -1.11 (0.46), residues: 134 loop : -0.44 (0.34), residues: 399 *********************** 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 108 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.836 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.1679 time to fit residues: 25.4517 Evaluate side-chains 99 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0829 time to fit residues: 1.6370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 47 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8469 Z= 0.177 Angle : 0.509 6.903 11869 Z= 0.258 Chirality : 0.037 0.188 1384 Planarity : 0.004 0.048 1229 Dihedral : 11.002 112.563 1828 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.59 % 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: 1.14 (0.31), residues: 271 sheet: -0.98 (0.46), residues: 132 loop : -0.40 (0.34), residues: 402 *********************** 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 98 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.819 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.2154 time to fit residues: 30.4535 Evaluate side-chains 92 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1097 time to fit residues: 2.5142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** C 47 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8469 Z= 0.210 Angle : 0.522 6.282 11869 Z= 0.266 Chirality : 0.037 0.185 1384 Planarity : 0.004 0.048 1229 Dihedral : 10.999 111.555 1828 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.59 % 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: 1.16 (0.32), residues: 269 sheet: -0.99 (0.46), residues: 134 loop : -0.38 (0.34), residues: 402 *********************** 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 100 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.800 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 98 average time/residue: 0.1782 time to fit residues: 25.0999 Evaluate side-chains 92 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0841 time to fit residues: 1.6796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0030 chunk 24 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 0.0670 chunk 79 optimal weight: 0.0670 chunk 52 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.2666 ------------------------------------------------------------------------------- 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** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8469 Z= 0.130 Angle : 0.483 6.189 11869 Z= 0.246 Chirality : 0.036 0.187 1384 Planarity : 0.004 0.047 1229 Dihedral : 10.732 108.822 1828 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.15 % 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: 0.15 (0.31), residues: 805 helix: 1.38 (0.32), residues: 271 sheet: -0.96 (0.45), residues: 137 loop : -0.32 (0.34), residues: 397 *********************** 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 98 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.813 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1886 time to fit residues: 26.1819 Evaluate side-chains 89 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8469 Z= 0.216 Angle : 0.531 7.170 11869 Z= 0.271 Chirality : 0.037 0.177 1384 Planarity : 0.004 0.046 1229 Dihedral : 10.807 108.253 1828 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.15 % 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: 1.19 (0.31), residues: 273 sheet: -0.90 (0.46), residues: 134 loop : -0.41 (0.34), residues: 398 ********************** 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 92 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.1891 time to fit residues: 24.6334 Evaluate side-chains 91 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1120 time to fit residues: 1.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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** ** D 35 GLN ** 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 = 0.4155 r_free = 0.4155 target = 0.161839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125506 restraints weight = 12372.760| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.43 r_work: 0.3508 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8469 Z= 0.150 Angle : 0.497 6.206 11869 Z= 0.253 Chirality : 0.036 0.182 1384 Planarity : 0.004 0.045 1229 Dihedral : 10.686 106.797 1828 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.15 % 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: 0.18 (0.31), residues: 805 helix: 1.36 (0.32), residues: 273 sheet: -0.76 (0.46), residues: 132 loop : -0.37 (0.34), residues: 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.47 seconds wall clock time: 34 minutes 12.85 seconds (2052.85 seconds total)