Starting phenix.real_space_refine (version: dev) on Sat Feb 18 12:53:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/02_2023/6jt2_9885_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/02_2023/6jt2_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_9885/02_2023/6jt2_9885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/02_2023/6jt2_9885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/02_2023/6jt2_9885_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/02_2023/6jt2_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 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-4877/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: 7.22, per 1000 atoms: 0.88 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: 3.42 Conformation dependent library (CDL) restraints added in 2.0 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: 1.04 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: 2.47 Time building geometry restraints manager: 3.70 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: 1.630 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: 3.520 Check model and map are aligned: 0.110 Process input model: 27.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.780 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- 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 : 10.08 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 : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 212 average time/residue: 0.1975 time to fit residues: 57.3459 Evaluate side-chains 112 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1180 time to fit residues: 3.2573 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.7140 ------------------------------------------------------------------------------- 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: 0.8075 moved from start: 0.2198 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= 0.208 Angle : 0.697 10.921 11367 Z= 0.342 Chirality : 0.043 0.219 1342 Planarity : 0.005 0.049 1431 Dihedral : 5.449 70.247 1152 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 3.07 % 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: -1.55 (0.24), residues: 1049 helix: -0.23 (0.22), residues: 488 sheet: -0.96 (0.35), residues: 204 loop : -2.04 (0.30), residues: 357 *********************** 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 141 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 135 average time/residue: 0.1676 time to fit residues: 33.1664 Evaluate side-chains 105 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0802 time to fit residues: 3.1022 ------------------------------------------------------------------------------- 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: 1.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 408 HIS B 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 8355 Z= 0.323 Angle : 0.691 10.282 11367 Z= 0.346 Chirality : 0.044 0.292 1342 Planarity : 0.005 0.052 1431 Dihedral : 5.363 62.052 1152 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer Outliers : 2.60 % 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: -1.16 (0.25), residues: 1049 helix: 0.01 (0.22), residues: 491 sheet: -0.61 (0.37), residues: 203 loop : -1.85 (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 123 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 117 average time/residue: 0.1513 time to fit residues: 27.0782 Evaluate side-chains 99 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1260 time to fit residues: 3.7161 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 B 171 ASN B 346 HIS 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: 0.8133 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8355 Z= 0.199 Angle : 0.622 11.512 11367 Z= 0.309 Chirality : 0.041 0.136 1342 Planarity : 0.004 0.048 1431 Dihedral : 5.242 64.265 1152 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.19 % Rotamer Outliers : 2.60 % 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: -0.89 (0.26), residues: 1049 helix: 0.29 (0.23), residues: 485 sheet: -0.60 (0.37), residues: 207 loop : -1.68 (0.32), 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 124 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 119 average time/residue: 0.1505 time to fit residues: 27.2861 Evaluate side-chains 100 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0875 time to fit residues: 2.9385 ------------------------------------------------------------------------------- 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: 0.0870 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN B 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3613 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= 0.195 Angle : 0.614 10.816 11367 Z= 0.303 Chirality : 0.040 0.140 1342 Planarity : 0.004 0.046 1431 Dihedral : 5.123 63.495 1152 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % 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: -0.66 (0.26), residues: 1049 helix: 0.47 (0.23), residues: 485 sheet: -0.50 (0.37), residues: 208 loop : -1.55 (0.32), residues: 356 *********************** 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 109 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 103 average time/residue: 0.1561 time to fit residues: 24.6549 Evaluate side-chains 93 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0774 time to fit residues: 2.0729 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.0030 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 8355 Z= 0.237 Angle : 0.629 10.924 11367 Z= 0.310 Chirality : 0.041 0.270 1342 Planarity : 0.004 0.050 1431 Dihedral : 5.071 60.350 1152 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.62 (0.26), residues: 1049 helix: 0.45 (0.23), residues: 494 sheet: -0.40 (0.37), residues: 208 loop : -1.55 (0.33), residues: 347 *********************** 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 113 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 107 average time/residue: 0.1487 time to fit residues: 24.3263 Evaluate side-chains 98 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0734 time to fit residues: 2.3318 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 86 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.4032 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= 0.161 Angle : 0.614 10.779 11367 Z= 0.297 Chirality : 0.040 0.213 1342 Planarity : 0.004 0.047 1431 Dihedral : 5.022 64.153 1152 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.83 % 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: -0.57 (0.26), residues: 1049 helix: 0.45 (0.23), residues: 490 sheet: -0.33 (0.37), residues: 212 loop : -1.47 (0.32), residues: 347 *********************** 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 99 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.000 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.1589 time to fit residues: 23.1510 Evaluate side-chains 89 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0888 time to fit residues: 1.8496 ------------------------------------------------------------------------------- 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: 0.7980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 89 optimal weight: 6.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8355 Z= 0.168 Angle : 0.613 11.111 11367 Z= 0.298 Chirality : 0.040 0.181 1342 Planarity : 0.004 0.048 1431 Dihedral : 4.958 63.768 1152 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.83 % 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: -0.43 (0.26), residues: 1049 helix: 0.54 (0.23), residues: 490 sheet: -0.18 (0.37), residues: 210 loop : -1.41 (0.32), residues: 349 *********************** 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 93 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.1556 time to fit residues: 21.5868 Evaluate side-chains 88 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0890 time to fit residues: 2.0564 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 90 optimal weight: 0.0060 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 overall best weight: 0.1952 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 8355 Z= 0.150 Angle : 0.613 11.669 11367 Z= 0.294 Chirality : 0.040 0.206 1342 Planarity : 0.004 0.047 1431 Dihedral : 4.872 66.038 1152 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.47 % 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: -0.37 (0.26), residues: 1049 helix: 0.57 (0.23), residues: 490 sheet: -0.04 (0.37), residues: 210 loop : -1.43 (0.32), 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: 4 poor density : 87 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 90 average time/residue: 0.1666 time to fit residues: 23.0095 Evaluate side-chains 86 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0968 time to fit residues: 1.5917 ------------------------------------------------------------------------------- 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: 0.0770 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4416 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= 0.221 Angle : 0.634 11.712 11367 Z= 0.305 Chirality : 0.041 0.225 1342 Planarity : 0.004 0.049 1431 Dihedral : 4.858 62.588 1152 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.35 % 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: -0.24 (0.26), residues: 1049 helix: 0.63 (0.23), residues: 493 sheet: 0.06 (0.38), residues: 210 loop : -1.35 (0.33), residues: 346 ********************** 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 87 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.1654 time to fit residues: 21.3325 Evaluate side-chains 83 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1015 time to fit residues: 1.4698 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083266 restraints weight = 22702.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085569 restraints weight = 15725.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.086354 restraints weight = 9930.990| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8355 Z= 0.196 Angle : 0.627 12.018 11367 Z= 0.301 Chirality : 0.041 0.238 1342 Planarity : 0.004 0.048 1431 Dihedral : 4.881 62.675 1152 Min Nonbonded Distance : 1.319 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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: -0.17 (0.26), residues: 1049 helix: 0.64 (0.23), residues: 488 sheet: 0.15 (0.38), residues: 209 loop : -1.24 (0.33), residues: 352 =============================================================================== Job complete usr+sys time: 1662.69 seconds wall clock time: 31 minutes 12.18 seconds (1872.18 seconds total)