Starting phenix.real_space_refine (version: 1.21rc1) on Fri Sep 29 22:42:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/09_2023/7zlj_14782_trim_updated.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 6223 2.51 5 N 1593 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 9659 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1679 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1598 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 5352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Conformer: "B" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} bond proxies already assigned to first conformer: 5464 Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Unusual residues: {'IZU': 1} Classifications: {'undetermined': 1, 'water': 9} Link IDs: {None: 9} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 214 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 214 " occ=0.50 Time building chain proxies: 7.95, per 1000 atoms: 0.82 Number of scatterers: 9659 At special positions: 0 Unit cell: (104.94, 165, 99.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1 15.00 O 1798 8.00 N 1593 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 650 " distance=2.03 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: 4.09 Conformation dependent library (CDL) restraints added in 2.2 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 13 sheets defined 35.9% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 203 through 206 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'L' and resid 123 through 126 removed outlier: 3.592A pdb=" N LEU L 126 " --> pdb=" O ASP L 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 126' Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.524A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'A' and resid 26 through 54 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 61 through 67 removed outlier: 4.174A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 removed outlier: 4.127A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 116 through 135 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 162 through 189 removed outlier: 4.228A pdb=" N THR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ALA A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 220 through 240 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.753A pdb=" N MET A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 263 through 282 removed outlier: 4.179A pdb=" N PHE A 269 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 273 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 276 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 277 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 278 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 320 through 336 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 342 through 368 removed outlier: 3.606A pdb=" N LYS A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 removed outlier: 4.087A pdb=" N LEU A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.621A pdb=" N THR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'A' and resid 450 through 468 removed outlier: 3.671A pdb=" N LEU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Proline residue: A 478 - end of helix removed outlier: 3.769A pdb=" N ALA A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 516 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 535 through 547 Processing helix chain 'A' and resid 558 through 566 removed outlier: 3.715A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 594 removed outlier: 4.068A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N MET A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE A 594 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.881A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'H' and resid 13 through 15 removed outlier: 5.714A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 135 through 139 Processing sheet with id= D, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.042A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.117A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 115 through 117 removed outlier: 5.594A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= H, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.598A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.772A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 115 through 119 Processing sheet with id= K, first strand: chain 'L' and resid 193 through 197 Processing sheet with id= L, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.713A pdb=" N LEU A 141 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 157 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 143 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 155 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 554 through 556 removed outlier: 5.831A pdb=" N TYR A 613 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 674 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS A 682 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE A 670 " --> pdb=" O LYS A 682 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1104 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: 2.86 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1613 1.32 - 1.47: 4023 1.47 - 1.61: 4188 1.61 - 1.75: 4 1.75 - 1.90: 67 Bond restraints: 9895 Sorted by residual: bond pdb=" CG PRO H 217 " pdb=" CD PRO H 217 " ideal model delta sigma weight residual 1.503 1.219 0.284 3.40e-02 8.65e+02 6.97e+01 bond pdb=" C PRO A 559 " pdb=" O PRO A 559 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.26e-02 6.30e+03 1.98e+01 bond pdb=" C MET A 558 " pdb=" O MET A 558 " ideal model delta sigma weight residual 1.244 1.209 0.034 9.80e-03 1.04e+04 1.21e+01 bond pdb=" C14 IZU A 801 " pdb=" C15 IZU A 801 " ideal model delta sigma weight residual 1.552 1.614 -0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" N VAL A 560 " pdb=" CA VAL A 560 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.63e+00 ... (remaining 9890 not shown) Histogram of bond angle deviations from ideal: 86.80 - 103.20: 88 103.20 - 119.59: 8276 119.59 - 135.99: 5080 135.99 - 152.39: 0 152.39 - 168.79: 2 Bond angle restraints: 13446 Sorted by residual: angle pdb=" C07 IZU A 801 " pdb=" C09 IZU A 801 " pdb=" C10 IZU A 801 " ideal model delta sigma weight residual 112.21 165.07 -52.86 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C12 IZU A 801 " pdb=" C14 IZU A 801 " pdb=" C15 IZU A 801 " ideal model delta sigma weight residual 120.02 168.79 -48.77 3.00e+00 1.11e-01 2.64e+02 angle pdb=" C08 IZU A 801 " pdb=" C07 IZU A 801 " pdb=" C09 IZU A 801 " ideal model delta sigma weight residual 85.87 133.37 -47.50 3.00e+00 1.11e-01 2.51e+02 angle pdb=" C01 IZU A 801 " pdb=" C02 IZU A 801 " pdb=" C03 IZU A 801 " ideal model delta sigma weight residual 74.51 118.84 -44.33 3.00e+00 1.11e-01 2.18e+02 angle pdb=" C06 IZU A 801 " pdb=" C07 IZU A 801 " pdb=" C08 IZU A 801 " ideal model delta sigma weight residual 68.16 105.80 -37.64 3.00e+00 1.11e-01 1.57e+02 ... (remaining 13441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 5637 31.16 - 62.32: 151 62.32 - 93.48: 14 93.48 - 124.64: 0 124.64 - 155.80: 1 Dihedral angle restraints: 5803 sinusoidal: 2232 harmonic: 3571 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 34.10 58.90 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual 93.00 44.99 48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CB CYS A 621 " pdb=" SG CYS A 621 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -43.53 -42.47 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 5800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 949 0.031 - 0.062: 382 0.062 - 0.093: 108 0.093 - 0.123: 64 0.123 - 0.154: 4 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA ARG K 19 " pdb=" N ARG K 19 " pdb=" C ARG K 19 " pdb=" CB ARG K 19 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA PRO A 641 " pdb=" N PRO A 641 " pdb=" C PRO A 641 " pdb=" CB PRO A 641 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" C PRO A 217 " pdb=" CB PRO A 217 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1504 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 216 " -0.074 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO H 217 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO H 217 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 217 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 640 " 0.062 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 641 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 163 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO H 164 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 164 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 164 " -0.031 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 116 2.61 - 3.18: 8966 3.18 - 3.75: 14289 3.75 - 4.33: 20281 4.33 - 4.90: 33333 Nonbonded interactions: 76985 Sorted by model distance: nonbonded pdb=" OG SER K 17 " pdb=" O MET K 83 " model vdw 2.033 2.440 nonbonded pdb=" NH1 ARG K 53 " pdb=" OG SER K 54 " model vdw 2.070 2.520 nonbonded pdb=" O ILE A 95 " pdb=" OG1 THR A 109 " model vdw 2.083 2.440 nonbonded pdb=" OG1 THR L 130 " pdb=" O LEU L 182 " model vdw 2.086 2.440 nonbonded pdb=" O LYS L 146 " pdb=" OG1 THR L 198 " model vdw 2.102 2.440 ... (remaining 76980 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.810 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: 13.440 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 32.490 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.005 0.284 9895 Z= 0.342 Angle : 1.151 52.859 13446 Z= 0.479 Chirality : 0.040 0.154 1507 Planarity : 0.005 0.105 1691 Dihedral : 13.958 155.802 3489 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 32.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.10 (0.25), residues: 1219 helix: 0.91 (0.26), residues: 456 sheet: 0.97 (0.33), residues: 223 loop : -1.07 (0.28), residues: 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2418 time to fit residues: 40.7050 Evaluate side-chains 97 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 61 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 620 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9895 Z= 0.210 Angle : 0.748 21.709 13446 Z= 0.340 Chirality : 0.044 0.143 1507 Planarity : 0.005 0.049 1691 Dihedral : 6.813 167.538 1340 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 0.66 % Allowed : 5.03 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.25), residues: 1219 helix: 1.14 (0.26), residues: 454 sheet: 1.05 (0.31), residues: 249 loop : -1.05 (0.28), residues: 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.101 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 0.2471 time to fit residues: 36.6563 Evaluate side-chains 100 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1024 time to fit residues: 2.1286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 527 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9895 Z= 0.191 Angle : 0.717 21.729 13446 Z= 0.326 Chirality : 0.043 0.142 1507 Planarity : 0.004 0.043 1691 Dihedral : 6.754 172.389 1340 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.47 % Allowed : 8.17 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.41 (0.25), residues: 1219 helix: 1.18 (0.26), residues: 458 sheet: 1.12 (0.31), residues: 243 loop : -0.96 (0.28), residues: 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 110 average time/residue: 0.2374 time to fit residues: 36.5586 Evaluate side-chains 102 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3387 time to fit residues: 2.3074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.0000 chunk 31 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9895 Z= 0.204 Angle : 0.715 21.429 13446 Z= 0.324 Chirality : 0.044 0.202 1507 Planarity : 0.004 0.039 1691 Dihedral : 6.938 171.822 1340 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.28 % Allowed : 10.35 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.49 (0.25), residues: 1219 helix: 1.24 (0.26), residues: 455 sheet: 1.11 (0.32), residues: 243 loop : -0.87 (0.28), residues: 521 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.106 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 103 average time/residue: 0.2317 time to fit residues: 33.8556 Evaluate side-chains 91 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9895 Z= 0.435 Angle : 0.808 21.469 13446 Z= 0.382 Chirality : 0.048 0.181 1507 Planarity : 0.005 0.046 1691 Dihedral : 7.155 171.937 1340 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.95 % Allowed : 10.54 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.03 (0.24), residues: 1219 helix: 0.63 (0.25), residues: 452 sheet: 0.97 (0.31), residues: 243 loop : -1.06 (0.28), residues: 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.226 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 111 average time/residue: 0.2238 time to fit residues: 35.5517 Evaluate side-chains 103 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1898 time to fit residues: 3.1946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9895 Z= 0.217 Angle : 0.724 21.461 13446 Z= 0.329 Chirality : 0.044 0.144 1507 Planarity : 0.004 0.041 1691 Dihedral : 6.888 168.993 1340 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.47 % Allowed : 12.16 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.25), residues: 1219 helix: 0.97 (0.26), residues: 455 sheet: 1.06 (0.31), residues: 243 loop : -1.04 (0.28), residues: 521 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.179 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 104 average time/residue: 0.2679 time to fit residues: 39.9514 Evaluate side-chains 100 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1207 time to fit residues: 2.2494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 0.0030 chunk 53 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9895 Z= 0.193 Angle : 0.714 21.763 13446 Z= 0.322 Chirality : 0.043 0.141 1507 Planarity : 0.004 0.037 1691 Dihedral : 6.708 167.451 1340 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.76 % Allowed : 11.87 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.36 (0.25), residues: 1219 helix: 1.16 (0.26), residues: 455 sheet: 1.07 (0.32), residues: 242 loop : -1.00 (0.28), residues: 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.131 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 104 average time/residue: 0.2331 time to fit residues: 34.3050 Evaluate side-chains 91 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1004 time to fit residues: 2.0306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9895 Z= 0.234 Angle : 0.730 21.802 13446 Z= 0.330 Chirality : 0.043 0.142 1507 Planarity : 0.004 0.048 1691 Dihedral : 6.713 166.875 1340 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.19 % Allowed : 12.92 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.29 (0.25), residues: 1219 helix: 1.09 (0.26), residues: 455 sheet: 1.09 (0.31), residues: 243 loop : -1.05 (0.28), residues: 521 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.188 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.2643 time to fit residues: 36.6343 Evaluate side-chains 91 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9895 Z= 0.203 Angle : 0.720 21.827 13446 Z= 0.324 Chirality : 0.043 0.141 1507 Planarity : 0.004 0.044 1691 Dihedral : 6.642 165.971 1340 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.19 % Allowed : 12.92 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.25), residues: 1219 helix: 1.18 (0.26), residues: 455 sheet: 1.12 (0.32), residues: 243 loop : -1.02 (0.28), residues: 521 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.140 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 91 average time/residue: 0.2496 time to fit residues: 31.9571 Evaluate side-chains 88 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5838 time to fit residues: 2.1288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9895 Z= 0.219 Angle : 0.729 21.853 13446 Z= 0.329 Chirality : 0.043 0.141 1507 Planarity : 0.004 0.041 1691 Dihedral : 6.632 165.435 1340 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.36 (0.25), residues: 1219 helix: 1.21 (0.26), residues: 449 sheet: 1.10 (0.31), residues: 243 loop : -1.04 (0.28), residues: 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2525 time to fit residues: 32.7890 Evaluate side-chains 90 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.172525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141910 restraints weight = 20090.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141483 restraints weight = 50906.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140560 restraints weight = 21044.484| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9895 Z= 0.223 Angle : 0.733 21.862 13446 Z= 0.332 Chirality : 0.043 0.144 1507 Planarity : 0.004 0.037 1691 Dihedral : 6.594 164.782 1340 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 0.09 % Allowed : 13.20 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.38 (0.25), residues: 1219 helix: 1.21 (0.26), residues: 449 sheet: 1.15 (0.32), residues: 243 loop : -1.03 (0.28), residues: 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.57 seconds wall clock time: 40 minutes 17.21 seconds (2417.21 seconds total)