Starting phenix.real_space_refine (version: dev) on Sat Feb 18 15:21:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2g_14465/02_2023/7z2g_14465_updated.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 Process input model Symmetric amino acids flipped Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8406 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4324 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3333 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2KW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.88, per 1000 atoms: 0.70 Number of scatterers: 8406 At special positions: 0 Unit cell: (98.94, 109.61, 97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 14 16.00 P 35 15.00 F 3 9.00 O 1629 8.00 N 1401 7.00 C 5323 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: 3.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 10 sheets defined 34.1% alpha, 12.8% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 removed outlier: 4.177A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.593A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TYR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.666A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.257A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.872A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.769A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.762A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.695A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.765A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.976A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.698A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.573A pdb=" N HIS B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 399 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.673A pdb=" N GLN A 145 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= D, first strand: chain 'A' and resid 326 through 331 removed outlier: 3.898A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 389 through 391 Processing sheet with id= F, first strand: chain 'A' and resid 464 through 470 removed outlier: 4.373A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 60 through 63 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.554A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 129 through 132 Processing sheet with id= J, first strand: chain 'B' and resid 414 through 416 removed outlier: 5.996A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1316 1.27 - 1.40: 2137 1.40 - 1.54: 5024 1.54 - 1.67: 193 1.67 - 1.81: 26 Bond restraints: 8696 Sorted by residual: bond pdb=" C10 2KW A 601 " pdb=" C9 2KW A 601 " ideal model delta sigma weight residual 1.354 1.522 -0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" C2 OMC E 4 " pdb=" N3 OMC E 4 " ideal model delta sigma weight residual 1.491 1.344 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C21 2KW A 601 " pdb=" N20 2KW A 601 " ideal model delta sigma weight residual 1.356 1.499 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C2 OMC E 2 " pdb=" N3 OMC E 2 " ideal model delta sigma weight residual 1.491 1.350 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C10 2KW A 601 " pdb=" N11 2KW A 601 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.51e+01 ... (remaining 8691 not shown) Histogram of bond angle deviations from ideal: 94.10 - 111.00: 3607 111.00 - 127.90: 8215 127.90 - 144.80: 152 144.80 - 161.70: 0 161.70 - 178.60: 1 Bond angle restraints: 11975 Sorted by residual: angle pdb=" C ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta sigma weight residual 109.38 94.10 15.28 2.03e+00 2.43e-01 5.67e+01 angle pdb=" C CYS A 63 " pdb=" CA CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sigma weight residual 109.66 120.31 -10.65 1.94e+00 2.66e-01 3.01e+01 angle pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" C ASP A 186 " ideal model delta sigma weight residual 109.06 117.88 -8.82 1.70e+00 3.46e-01 2.69e+01 angle pdb=" N GLY B 155 " pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 113.86 107.18 6.68 1.50e+00 4.44e-01 1.98e+01 angle pdb=" C5' DG E 33 " pdb=" C4' DG E 33 " pdb=" O4' DG E 33 " ideal model delta sigma weight residual 109.40 115.87 -6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 11970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4318 17.27 - 34.55: 553 34.55 - 51.82: 161 51.82 - 69.09: 46 69.09 - 86.37: 12 Dihedral angle restraints: 5090 sinusoidal: 2339 harmonic: 2751 Sorted by residual: dihedral pdb=" C ASP A 186 " pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta harmonic sigma weight residual -122.60 -107.57 -15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" CA ILE A 411 " pdb=" C ILE A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE A 77 " pdb=" C PHE A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1177 0.083 - 0.166: 111 0.166 - 0.249: 7 0.249 - 0.332: 1 0.332 - 0.415: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" C4' DG E 32 " pdb=" C5' DG E 32 " pdb=" O4' DG E 32 " pdb=" C3' DG E 32 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C4' DG E 33 " pdb=" C5' DG E 33 " pdb=" O4' DG E 33 " pdb=" C3' DG E 33 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C4' DC E 22 " pdb=" C5' DC E 22 " pdb=" O4' DC E 22 " pdb=" C3' DC E 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1295 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 2 " 0.045 2.00e-02 2.50e+03 5.85e-01 7.69e+03 pdb=" C4' OMC E 2 " -0.479 2.00e-02 2.50e+03 pdb=" O4' OMC E 2 " -0.797 2.00e-02 2.50e+03 pdb=" C3' OMC E 2 " 0.577 2.00e-02 2.50e+03 pdb=" O3' OMC E 2 " 0.515 2.00e-02 2.50e+03 pdb=" C2' OMC E 2 " 0.260 2.00e-02 2.50e+03 pdb=" O2' OMC E 2 " -0.813 2.00e-02 2.50e+03 pdb=" C1' OMC E 2 " -0.221 2.00e-02 2.50e+03 pdb=" N1 OMC E 2 " 0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 4 " 0.010 2.00e-02 2.50e+03 5.60e-01 7.05e+03 pdb=" C4' OMC E 4 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMC E 4 " 0.538 2.00e-02 2.50e+03 pdb=" C3' OMC E 4 " -0.612 2.00e-02 2.50e+03 pdb=" O3' OMC E 4 " -0.570 2.00e-02 2.50e+03 pdb=" C2' OMC E 4 " -0.185 2.00e-02 2.50e+03 pdb=" O2' OMC E 4 " 0.938 2.00e-02 2.50e+03 pdb=" C1' OMC E 4 " 0.264 2.00e-02 2.50e+03 pdb=" N1 OMC E 4 " -0.814 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 358 " 0.492 9.50e-02 1.11e+02 2.20e-01 2.97e+01 pdb=" NE ARG A 358 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 358 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 358 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 358 " 0.017 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2637 2.84 - 3.35: 7497 3.35 - 3.87: 13792 3.87 - 4.38: 16062 4.38 - 4.90: 26817 Nonbonded interactions: 66805 Sorted by model distance: nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 39 " model vdw 2.324 2.440 nonbonded pdb=" O PHE A 77 " pdb=" N ASN A 81 " model vdw 2.327 2.520 nonbonded pdb=" OH TYR B 115 " pdb=" OE1 GLN B 182 " model vdw 2.360 2.440 nonbonded pdb=" OG1 THR A 107 " pdb=" NE2 HIS A 198 " model vdw 2.371 2.520 nonbonded pdb=" O LYS B 366 " pdb=" OE1 GLU B 370 " model vdw 2.382 3.040 ... (remaining 66800 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 35 5.49 5 S 14 5.16 5 Cl 1 4.86 5 C 5323 2.51 5 N 1401 2.21 5 O 1629 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.090 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: 1.200 Check model and map are aligned: 0.120 Process input model: 28.440 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.007 0.168 8696 Z= 0.439 Angle : 0.728 15.282 11975 Z= 0.409 Chirality : 0.049 0.415 1298 Planarity : 0.023 0.585 1390 Dihedral : 17.043 86.367 3314 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.03 % 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: -0.62 (0.27), residues: 931 helix: 0.63 (0.31), residues: 316 sheet: -0.91 (0.40), residues: 151 loop : -0.91 (0.28), residues: 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.016 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.1846 time to fit residues: 30.7438 Evaluate side-chains 83 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 8696 Z= 0.316 Angle : 0.732 13.295 11975 Z= 0.413 Chirality : 0.044 0.177 1298 Planarity : 0.007 0.127 1390 Dihedral : 16.512 100.029 1364 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.65 (0.27), residues: 931 helix: 0.61 (0.30), residues: 319 sheet: -1.01 (0.39), residues: 154 loop : -0.91 (0.29), residues: 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.859 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 101 average time/residue: 0.1846 time to fit residues: 26.9651 Evaluate side-chains 95 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0787 time to fit residues: 2.6661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 8696 Z= 0.350 Angle : 0.746 12.947 11975 Z= 0.420 Chirality : 0.045 0.184 1298 Planarity : 0.007 0.120 1390 Dihedral : 16.681 95.853 1364 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.87 (0.27), residues: 931 helix: 0.40 (0.30), residues: 325 sheet: -0.91 (0.40), residues: 147 loop : -1.13 (0.28), residues: 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.889 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 103 average time/residue: 0.1861 time to fit residues: 27.8049 Evaluate side-chains 94 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0812 time to fit residues: 2.3969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8696 Z= 0.212 Angle : 0.687 13.098 11975 Z= 0.394 Chirality : 0.042 0.154 1298 Planarity : 0.006 0.117 1390 Dihedral : 16.428 93.320 1364 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.28), residues: 931 helix: 0.65 (0.30), residues: 325 sheet: -0.79 (0.40), residues: 149 loop : -0.93 (0.29), residues: 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.939 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.1754 time to fit residues: 26.7117 Evaluate side-chains 95 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0766 time to fit residues: 2.6267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8696 Z= 0.244 Angle : 0.688 12.862 11975 Z= 0.395 Chirality : 0.043 0.258 1298 Planarity : 0.006 0.118 1390 Dihedral : 16.410 93.175 1364 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.58 (0.27), residues: 931 helix: 0.71 (0.30), residues: 326 sheet: -0.90 (0.39), residues: 154 loop : -0.96 (0.29), residues: 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.975 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 0.2005 time to fit residues: 28.7216 Evaluate side-chains 91 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0830 time to fit residues: 1.9428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8696 Z= 0.223 Angle : 0.679 12.775 11975 Z= 0.391 Chirality : 0.042 0.216 1298 Planarity : 0.006 0.118 1390 Dihedral : 16.456 92.997 1364 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.51 (0.27), residues: 931 helix: 0.75 (0.30), residues: 326 sheet: -0.72 (0.40), residues: 149 loop : -0.96 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.810 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.1881 time to fit residues: 26.3298 Evaluate side-chains 89 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0919 time to fit residues: 2.2895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8696 Z= 0.181 Angle : 0.667 12.813 11975 Z= 0.386 Chirality : 0.041 0.195 1298 Planarity : 0.006 0.117 1390 Dihedral : 16.426 93.399 1364 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.28), residues: 931 helix: 0.80 (0.30), residues: 329 sheet: -0.60 (0.40), residues: 149 loop : -0.94 (0.29), residues: 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.925 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.1946 time to fit residues: 27.9846 Evaluate side-chains 91 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0774 time to fit residues: 1.5963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 334 GLN A 524 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 8696 Z= 0.369 Angle : 0.749 12.613 11975 Z= 0.419 Chirality : 0.045 0.180 1298 Planarity : 0.006 0.121 1390 Dihedral : 16.758 87.504 1364 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.76 (0.27), residues: 931 helix: 0.56 (0.30), residues: 326 sheet: -0.88 (0.40), residues: 149 loop : -1.12 (0.28), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.000 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 88 average time/residue: 0.2048 time to fit residues: 25.9294 Evaluate side-chains 83 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0781 time to fit residues: 1.9665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8696 Z= 0.251 Angle : 0.698 12.662 11975 Z= 0.397 Chirality : 0.042 0.172 1298 Planarity : 0.006 0.119 1390 Dihedral : 16.632 87.476 1364 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.60 (0.27), residues: 931 helix: 0.71 (0.30), residues: 328 sheet: -0.89 (0.40), residues: 149 loop : -1.01 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.928 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 93 average time/residue: 0.2192 time to fit residues: 28.7392 Evaluate side-chains 89 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0925 time to fit residues: 1.9937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8696 Z= 0.241 Angle : 0.703 12.646 11975 Z= 0.399 Chirality : 0.042 0.180 1298 Planarity : 0.006 0.119 1390 Dihedral : 16.522 86.441 1364 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 931 helix: 0.60 (0.30), residues: 330 sheet: -0.86 (0.40), residues: 149 loop : -1.02 (0.29), residues: 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.955 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2083 time to fit residues: 27.4011 Evaluate side-chains 86 residues out of total 847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.0170 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 HIS ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.194515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.164891 restraints weight = 9047.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.160550 restraints weight = 13606.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.160547 restraints weight = 11684.578| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8696 Z= 0.166 Angle : 0.670 12.779 11975 Z= 0.386 Chirality : 0.041 0.188 1298 Planarity : 0.006 0.117 1390 Dihedral : 16.332 87.639 1364 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.28), residues: 931 helix: 0.89 (0.30), residues: 330 sheet: -0.62 (0.40), residues: 149 loop : -0.91 (0.29), residues: 452 =============================================================================== Job complete usr+sys time: 1409.74 seconds wall clock time: 26 minutes 59.36 seconds (1619.36 seconds total)