Starting phenix.real_space_refine (version: dev) on Sun Dec 11 23:51:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/12_2022/6jt2_9885_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/12_2022/6jt2_9885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/12_2022/6jt2_9885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/12_2022/6jt2_9885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/12_2022/6jt2_9885_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/12_2022/6jt2_9885_updated.pdb" } resolution = 3.8 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8191 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3742 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 8 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 4372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 4452 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 Time building chain proxies: 7.29, per 1000 atoms: 0.89 Number of scatterers: 8191 At special positions: 0 Unit cell: (147.345, 87.78, 98.23, 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) Fe 1 26.01 S 56 16.00 P 3 15.00 Mg 2 11.99 O 1475 8.00 N 1392 7.00 C 5262 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: 3.34 Conformation dependent library (CDL) restraints added in 2.2 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 9 sheets defined 44.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 148 removed outlier: 3.730A pdb=" N GLU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.800A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.762A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.643A pdb=" N LYS A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 409 through 457 Processing helix chain 'A' and resid 460 through 467 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.517A pdb=" N GLN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 4.084A pdb=" N GLU A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.642A pdb=" N ASN A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 94 through 111 removed outlier: 4.732A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 265 through 270 removed outlier: 3.892A pdb=" N SER B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 348 through 397 removed outlier: 4.349A pdb=" N VAL B 353 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 357 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.412A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 566 through 572 Processing sheet with id= A, first strand: chain 'A' and resid 201 through 204 Processing sheet with id= B, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.649A pdb=" N GLN A 300 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= D, first strand: chain 'A' and resid 523 through 525 removed outlier: 4.409A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 615 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU A 577 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN A 617 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N SER A 579 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 634 through 636 Processing sheet with id= F, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.896A pdb=" N GLN B 168 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLU B 182 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N MET B 164 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.754A pdb=" N ARG B 258 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG B 279 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU B 256 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.532A pdb=" N GLY B 531 " --> pdb=" O CYS B 541 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 469 through 474 removed outlier: 7.068A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 474 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR B 525 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3335 1.39 - 1.56: 4924 1.56 - 1.73: 6 1.73 - 1.90: 86 1.90 - 2.07: 4 Bond restraints: 8355 Sorted by residual: bond pdb=" O3B G2P A1001 " pdb=" PG G2P A1001 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O1A G2P A1001 " pdb=" PA G2P A1001 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O1B G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C4 G2P A1001 " pdb=" C5 G2P A1001 " ideal model delta sigma weight residual 1.384 1.469 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 G2P A1001 " pdb=" C6 G2P A1001 " ideal model delta sigma weight residual 1.420 1.483 -0.063 2.00e-02 2.50e+03 9.79e+00 ... (remaining 8350 not shown) Histogram of bond angle deviations from ideal: 88.58 - 106.57: 253 106.57 - 124.57: 10970 124.57 - 142.56: 142 142.56 - 160.55: 0 160.55 - 178.54: 2 Bond angle restraints: 11367 Sorted by residual: angle pdb=" PA G2P A1001 " pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 120.83 109.47 11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " pdb=" O3B G2P A1001 " ideal model delta sigma weight residual 99.71 109.82 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C5 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N3 G2P A1001 " ideal model delta sigma weight residual 128.08 118.69 9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.28e+00 angle pdb=" C3A G2P A1001 " pdb=" PA G2P A1001 " pdb=" O5' G2P A1001 " ideal model delta sigma weight residual 99.14 108.27 -9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 11362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 4662 16.26 - 32.52: 229 32.52 - 48.78: 55 48.78 - 65.03: 14 65.03 - 81.29: 4 Dihedral angle restraints: 4964 sinusoidal: 1841 harmonic: 3123 Sorted by residual: dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR B 339 " pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta harmonic sigma weight residual 180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE A 301 " pdb=" C PHE A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1106 0.055 - 0.111: 213 0.111 - 0.166: 22 0.166 - 0.221: 0 0.221 - 0.276: 1 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL A 462 " pdb=" CA VAL A 462 " pdb=" CG1 VAL A 462 " pdb=" CG2 VAL A 462 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA VAL A 462 " pdb=" N VAL A 462 " pdb=" C VAL A 462 " pdb=" CB VAL A 462 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C2' G2P A1001 " pdb=" C1' G2P A1001 " pdb=" C3' G2P A1001 " pdb=" O2' G2P A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1339 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C VAL A 462 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 462 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 463 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 258 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO B 259 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 209 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 210 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.031 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 50 2.56 - 3.15: 6549 3.15 - 3.73: 12636 3.73 - 4.32: 16594 4.32 - 4.90: 27833 Nonbonded interactions: 63662 Sorted by model distance: nonbonded pdb=" O2B G2P A1001 " pdb="MG MG A1002 " model vdw 1.980 2.170 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1002 " model vdw 2.095 2.170 nonbonded pdb=" OD2 ASP A 486 " pdb="MG MG A1002 " model vdw 2.101 2.170 nonbonded pdb=" O5' G2P A1001 " pdb="MG MG A1003 " model vdw 2.172 2.170 nonbonded pdb=" O LEU A 520 " pdb=" NE2 GLN A 548 " model vdw 2.259 2.520 ... (remaining 63657 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 Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1475 1.98 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=0.30 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: 0.950 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: 3.880 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 29.480 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.004 0.106 8355 Z= 0.290 Angle : 0.738 11.357 11367 Z= 0.377 Chirality : 0.042 0.276 1342 Planarity : 0.005 0.058 1431 Dihedral : 11.139 81.292 2938 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.00 % Favored : 95.71 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.23), residues: 1049 helix: -1.24 (0.20), residues: 478 sheet: -1.17 (0.35), residues: 192 loop : -2.34 (0.28), residues: 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 212 average time/residue: 0.1872 time to fit residues: 54.5755 Evaluate side-chains 112 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1193 time to fit residues: 3.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 96 optimal weight: 10.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 408 HIS B 491 HIS B 548 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8355 Z= 0.209 Angle : 0.696 11.125 11367 Z= 0.342 Chirality : 0.043 0.183 1342 Planarity : 0.005 0.050 1431 Dihedral : 5.454 70.135 1152 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1049 helix: -0.24 (0.22), residues: 487 sheet: -0.96 (0.35), residues: 204 loop : -2.06 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 131 average time/residue: 0.1585 time to fit residues: 30.8276 Evaluate side-chains 107 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0832 time to fit residues: 3.1406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS B 408 HIS B 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 8355 Z= 0.209 Angle : 0.633 10.097 11367 Z= 0.313 Chirality : 0.042 0.292 1342 Planarity : 0.004 0.050 1431 Dihedral : 5.250 66.237 1152 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.81 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1049 helix: 0.12 (0.22), residues: 487 sheet: -0.67 (0.36), residues: 207 loop : -1.89 (0.31), residues: 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.1421 time to fit residues: 24.4642 Evaluate side-chains 102 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0758 time to fit residues: 2.9674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 422 GLN A 516 GLN B 171 ASN B 448 ASN B 451 ASN B 563 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8355 Z= 0.200 Angle : 0.620 11.457 11367 Z= 0.304 Chirality : 0.041 0.189 1342 Planarity : 0.004 0.048 1431 Dihedral : 5.130 65.184 1152 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.85 (0.25), residues: 1049 helix: 0.32 (0.23), residues: 486 sheet: -0.55 (0.36), residues: 206 loop : -1.70 (0.31), residues: 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 112 average time/residue: 0.1564 time to fit residues: 26.5841 Evaluate side-chains 100 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0823 time to fit residues: 2.4111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 8355 Z= 0.210 Angle : 0.612 9.888 11367 Z= 0.302 Chirality : 0.040 0.136 1342 Planarity : 0.004 0.047 1431 Dihedral : 5.035 63.966 1152 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.19 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.64 (0.26), residues: 1049 helix: 0.51 (0.23), residues: 481 sheet: -0.42 (0.37), residues: 207 loop : -1.60 (0.31), residues: 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.1478 time to fit residues: 23.3305 Evaluate side-chains 95 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1260 time to fit residues: 2.9454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8355 Z= 0.191 Angle : 0.612 9.953 11367 Z= 0.299 Chirality : 0.041 0.263 1342 Planarity : 0.004 0.047 1431 Dihedral : 5.027 64.004 1152 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.63 (0.25), residues: 1049 helix: 0.48 (0.23), residues: 487 sheet: -0.39 (0.36), residues: 211 loop : -1.61 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.073 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 105 average time/residue: 0.1516 time to fit residues: 24.7376 Evaluate side-chains 94 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0796 time to fit residues: 2.1966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.0170 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 8355 Z= 0.176 Angle : 0.607 10.710 11367 Z= 0.295 Chirality : 0.041 0.224 1342 Planarity : 0.004 0.047 1431 Dihedral : 4.956 63.466 1152 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.25), residues: 1049 helix: 0.49 (0.23), residues: 491 sheet: -0.30 (0.36), residues: 210 loop : -1.57 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 0.1527 time to fit residues: 22.2801 Evaluate side-chains 88 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0771 time to fit residues: 2.0699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 69 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 0.0010 chunk 89 optimal weight: 5.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- 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: 0.8101 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 8355 Z= 0.164 Angle : 0.609 10.715 11367 Z= 0.296 Chirality : 0.040 0.225 1342 Planarity : 0.004 0.050 1431 Dihedral : 4.921 64.682 1152 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.42 (0.25), residues: 1049 helix: 0.57 (0.23), residues: 491 sheet: -0.19 (0.37), residues: 210 loop : -1.46 (0.32), residues: 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.1509 time to fit residues: 20.7060 Evaluate side-chains 89 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0801 time to fit residues: 1.6598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 8355 Z= 0.219 Angle : 0.633 11.019 11367 Z= 0.306 Chirality : 0.041 0.260 1342 Planarity : 0.004 0.049 1431 Dihedral : 4.954 62.164 1152 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1049 helix: 0.61 (0.23), residues: 490 sheet: -0.09 (0.37), residues: 210 loop : -1.40 (0.33), residues: 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 0.1609 time to fit residues: 21.4035 Evaluate side-chains 90 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0832 time to fit residues: 2.2180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8355 Z= 0.178 Angle : 0.628 11.371 11367 Z= 0.301 Chirality : 0.041 0.236 1342 Planarity : 0.004 0.050 1431 Dihedral : 4.930 63.817 1152 Min Nonbonded Distance : 1.453 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1049 helix: 0.58 (0.23), residues: 488 sheet: 0.02 (0.37), residues: 210 loop : -1.39 (0.32), residues: 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.1599 time to fit residues: 20.8670 Evaluate side-chains 86 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1033 time to fit residues: 1.5471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083470 restraints weight = 22645.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085728 restraints weight = 16051.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086440 restraints weight = 10431.680| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8355 Z= 0.190 Angle : 0.623 11.046 11367 Z= 0.299 Chirality : 0.041 0.249 1342 Planarity : 0.004 0.049 1431 Dihedral : 4.895 62.999 1152 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1049 helix: 0.68 (0.23), residues: 482 sheet: 0.09 (0.37), residues: 210 loop : -1.33 (0.32), residues: 357 =============================================================================== Job complete usr+sys time: 1660.32 seconds wall clock time: 31 minutes 3.74 seconds (1863.74 seconds total)