Starting phenix.real_space_refine on Wed Feb 14 15:47:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlg_14779/02_2024/7zlg_14779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlg_14779/02_2024/7zlg_14779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlg_14779/02_2024/7zlg_14779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlg_14779/02_2024/7zlg_14779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlg_14779/02_2024/7zlg_14779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlg_14779/02_2024/7zlg_14779.pdb" } resolution = 2.72 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6191 2.51 5 N 1593 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9618 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} 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: 7.68, per 1000 atoms: 0.80 Number of scatterers: 9618 At special positions: 0 Unit cell: (101.64, 162.36, 97.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1790 8.00 N 1593 7.00 C 6191 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=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 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=2.04 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: 3.60 Conformation dependent library (CDL) restraints added in 2.6 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... Secondary structure from input PDB file: 43 helices and 14 sheets defined 42.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 207 removed outlier: 3.988A pdb=" N GLN H 207 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.993A pdb=" N GLN K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'L' and resid 122 through 127 removed outlier: 4.199A pdb=" N LEU L 126 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS L 127 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.890A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 Processing helix chain 'A' and resid 56 through 59 removed outlier: 3.550A pdb=" N LEU A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 71 through 85 removed outlier: 4.037A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 115 through 135 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 161 through 188 removed outlier: 4.080A pdb=" N THR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.762A pdb=" N GLY A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 218 through 241 removed outlier: 3.933A pdb=" N PHE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.616A 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 264 through 281 Processing helix chain 'A' and resid 286 through 308 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.576A pdb=" N SER A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.579A pdb=" N PHE A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.604A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 436 Processing helix chain 'A' and resid 449 through 469 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.554A pdb=" N MET A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.536A pdb=" N ALA A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 500 through 517 Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 534 through 548 removed outlier: 4.149A pdb=" N GLU A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.652A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 619 through 622 removed outlier: 3.862A pdb=" N SER A 622 " --> pdb=" O MET A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 631 through 640 removed outlier: 4.034A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.652A pdb=" N LEU A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.777A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.744A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.244A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL H 196 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS H 179 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.244A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.073A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.431A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP K 99 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE K 98 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP K 109 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.431A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP K 99 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.618A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.222A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AB4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AB5, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.505A pdb=" N ALA A 555 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLN A 617 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR A 678 " --> pdb=" O ASN A 673 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN A 673 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 680 " --> pdb=" O VAL A 671 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1395 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: 2.87 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1516 1.32 - 1.44: 2869 1.44 - 1.57: 5403 1.57 - 1.69: 0 1.69 - 1.82: 66 Bond restraints: 9854 Sorted by residual: bond pdb=" CG PRO H 44 " pdb=" CD PRO H 44 " ideal model delta sigma weight residual 1.503 1.239 0.264 3.40e-02 8.65e+02 6.02e+01 bond pdb=" C THR A 70 " pdb=" O THR A 70 " ideal model delta sigma weight residual 1.236 1.195 0.042 1.15e-02 7.56e+03 1.31e+01 bond pdb=" N VAL A 581 " pdb=" CA VAL A 581 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.23e+01 bond pdb=" N HIS A 580 " pdb=" CA HIS A 580 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.20e-02 6.94e+03 1.14e+01 bond pdb=" N ARG A 471 " pdb=" CA ARG A 471 " ideal model delta sigma weight residual 1.460 1.503 -0.043 1.28e-02 6.10e+03 1.14e+01 ... (remaining 9849 not shown) Histogram of bond angle deviations from ideal: 83.71 - 93.84: 2 93.84 - 103.97: 119 103.97 - 114.10: 5729 114.10 - 124.23: 7298 124.23 - 134.36: 244 Bond angle restraints: 13392 Sorted by residual: angle pdb=" N PRO H 44 " pdb=" CD PRO H 44 " pdb=" CG PRO H 44 " ideal model delta sigma weight residual 103.20 84.45 18.75 1.50e+00 4.44e-01 1.56e+02 angle pdb=" CA PRO H 44 " pdb=" CB PRO H 44 " pdb=" CG PRO H 44 " ideal model delta sigma weight residual 104.50 83.71 20.79 1.90e+00 2.77e-01 1.20e+02 angle pdb=" N THR A 70 " pdb=" CA THR A 70 " pdb=" C THR A 70 " ideal model delta sigma weight residual 111.07 120.40 -9.33 1.07e+00 8.73e-01 7.60e+01 angle pdb=" N PRO H 44 " pdb=" CA PRO H 44 " pdb=" CB PRO H 44 " ideal model delta sigma weight residual 103.27 97.33 5.94 9.00e-01 1.23e+00 4.36e+01 angle pdb=" N LEU A 472 " pdb=" CA LEU A 472 " pdb=" C LEU A 472 " ideal model delta sigma weight residual 113.17 105.23 7.94 1.26e+00 6.30e-01 3.97e+01 ... (remaining 13387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5319 17.70 - 35.39: 381 35.39 - 53.09: 65 53.09 - 70.78: 15 70.78 - 88.48: 12 Dihedral angle restraints: 5792 sinusoidal: 2221 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 30.80 62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CA GLU A 629 " pdb=" C GLU A 629 " pdb=" N CYS A 630 " pdb=" CA CYS A 630 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA SER H 108 " pdb=" C SER H 108 " pdb=" N TRP H 109 " pdb=" CA TRP H 109 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 5789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1095 0.045 - 0.090: 311 0.090 - 0.135: 84 0.135 - 0.180: 7 0.180 - 0.225: 4 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA ILE A 469 " pdb=" N ILE A 469 " pdb=" C ILE A 469 " pdb=" CB ILE A 469 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 470 " pdb=" N MET A 470 " pdb=" C MET A 470 " pdb=" CB MET A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 1498 not shown) Planarity restraints: 1687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 473 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.65e+00 pdb=" C LYS A 473 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 473 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 474 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 261 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C PHE A 261 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE A 261 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP A 262 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 68 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C TYR A 68 " 0.042 2.00e-02 2.50e+03 pdb=" O TYR A 68 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 69 " -0.014 2.00e-02 2.50e+03 ... (remaining 1684 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 486 2.73 - 3.27: 9590 3.27 - 3.81: 15516 3.81 - 4.36: 18748 4.36 - 4.90: 32213 Nonbonded interactions: 76553 Sorted by model distance: nonbonded pdb=" O ALA A 388 " pdb=" OG1 THR A 392 " model vdw 2.187 2.440 nonbonded pdb=" OD2 ASP A 640 " pdb=" ND2 ASN A 643 " model vdw 2.212 2.520 nonbonded pdb=" OH TYR A 116 " pdb=" O LEU A 307 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR L 130 " pdb=" O LEU L 182 " model vdw 2.252 2.440 nonbonded pdb=" NH1 ARG A 342 " pdb=" O ASN A 437 " model vdw 2.261 2.520 ... (remaining 76548 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 12.820 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.880 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.264 9854 Z= 0.292 Angle : 0.713 20.789 13392 Z= 0.421 Chirality : 0.045 0.225 1501 Planarity : 0.004 0.048 1687 Dihedral : 13.430 88.479 3478 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.36 % Favored : 95.23 % Rotamer: Outliers : 0.66 % Allowed : 0.47 % Favored : 98.86 % 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 (0.25), residues: 1219 helix: 1.06 (0.26), residues: 444 sheet: 0.91 (0.34), residues: 254 loop : -1.38 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 0 HIS 0.003 0.001 HIS A 375 PHE 0.013 0.001 PHE A 348 TYR 0.016 0.001 TYR H 83 ARG 0.005 0.000 ARG A 393 *********************** 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 123 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 44 PRO cc_start: 0.4930 (OUTLIER) cc_final: 0.4540 (Cg_endo) REVERT: H 86 MET cc_start: 0.5848 (mpp) cc_final: 0.5559 (mpp) REVERT: L 5 MET cc_start: 0.4857 (mmm) cc_final: 0.4531 (mtp) REVERT: L 38 GLN cc_start: 0.5500 (tt0) cc_final: 0.5241 (tt0) REVERT: A 561 MET cc_start: 0.8716 (mmp) cc_final: 0.8476 (mmp) outliers start: 7 outliers final: 1 residues processed: 122 average time/residue: 1.2645 time to fit residues: 165.1598 Evaluate side-chains 94 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 44 PRO Chi-restraints excluded: chain A residue 70 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 50.0000 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 156 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 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: 0.8039 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9854 Z= 0.237 Angle : 0.614 9.081 13392 Z= 0.322 Chirality : 0.046 0.167 1501 Planarity : 0.005 0.065 1687 Dihedral : 4.492 36.371 1333 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.26 % Favored : 94.41 % Rotamer: Outliers : 1.14 % Allowed : 7.60 % Favored : 91.26 % 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: 0.19 (0.25), residues: 1219 helix: 1.25 (0.25), residues: 456 sheet: 0.97 (0.34), residues: 251 loop : -1.39 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 110 HIS 0.006 0.001 HIS A 391 PHE 0.016 0.002 PHE A 320 TYR 0.023 0.002 TYR H 83 ARG 0.007 0.001 ARG A 393 *********************** 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 108 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.5986 (mpp) cc_final: 0.5761 (mpp) REVERT: H 160 TYR cc_start: 0.3510 (p90) cc_final: 0.2942 (p90) REVERT: L 5 MET cc_start: 0.4863 (mmm) cc_final: 0.4642 (mtp) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 1.2217 time to fit residues: 138.9337 Evaluate side-chains 100 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 297 HIS A 375 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9854 Z= 0.221 Angle : 0.587 9.074 13392 Z= 0.309 Chirality : 0.045 0.160 1501 Planarity : 0.004 0.050 1687 Dihedral : 4.480 43.206 1330 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 1.61 % Allowed : 9.59 % Favored : 88.79 % 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: 0.23 (0.25), residues: 1219 helix: 1.41 (0.25), residues: 456 sheet: 0.81 (0.34), residues: 254 loop : -1.39 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.013 0.001 PHE A 387 TYR 0.016 0.001 TYR A 319 ARG 0.006 0.000 ARG A 393 *********************** 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: 17 poor density : 96 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.5957 (mpp) cc_final: 0.5659 (mpp) REVERT: H 160 TYR cc_start: 0.3445 (p90) cc_final: 0.2910 (p90) REVERT: L 38 GLN cc_start: 0.5404 (tt0) cc_final: 0.5070 (tt0) REVERT: A 71 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6262 (pt0) REVERT: A 154 GLU cc_start: 0.7788 (tt0) cc_final: 0.7526 (tt0) REVERT: A 542 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7482 (m-30) outliers start: 17 outliers final: 7 residues processed: 108 average time/residue: 1.2098 time to fit residues: 141.4332 Evaluate side-chains 99 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.0370 chunk 116 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 50.0000 chunk 97 optimal weight: 0.0770 overall best weight: 0.8818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN A 643 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: 0.8030 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 9854 Z= 0.217 Angle : 0.600 15.864 13392 Z= 0.311 Chirality : 0.045 0.245 1501 Planarity : 0.004 0.047 1687 Dihedral : 4.490 49.876 1330 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 1.61 % Allowed : 11.21 % Favored : 87.18 % 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: 1.57 (0.25), residues: 454 sheet: 0.90 (0.34), residues: 253 loop : -1.36 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 440 HIS 0.004 0.001 HIS A 391 PHE 0.012 0.001 PHE A 320 TYR 0.016 0.001 TYR A 319 ARG 0.005 0.000 ARG A 393 *********************** 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 108 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.5999 (mpp) cc_final: 0.5672 (mpp) REVERT: H 160 TYR cc_start: 0.3318 (p90) cc_final: 0.2769 (p90) REVERT: L 5 MET cc_start: 0.5022 (mmm) cc_final: 0.4766 (mtp) REVERT: L 38 GLN cc_start: 0.5397 (tt0) cc_final: 0.5057 (tt0) REVERT: A 71 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6250 (pt0) REVERT: A 434 LYS cc_start: 0.7548 (mmtm) cc_final: 0.7127 (tttp) REVERT: A 542 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7475 (m-30) outliers start: 17 outliers final: 8 residues processed: 101 average time/residue: 1.4200 time to fit residues: 154.2101 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 9854 Z= 0.399 Angle : 0.705 16.618 13392 Z= 0.371 Chirality : 0.050 0.246 1501 Planarity : 0.005 0.067 1687 Dihedral : 4.960 58.974 1330 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.76 % Favored : 93.83 % Rotamer: Outliers : 1.61 % Allowed : 12.92 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.01 (0.24), residues: 1219 helix: 1.14 (0.25), residues: 450 sheet: 0.69 (0.33), residues: 255 loop : -1.40 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 109 HIS 0.007 0.002 HIS A 391 PHE 0.018 0.002 PHE A 224 TYR 0.017 0.002 TYR A 319 ARG 0.007 0.001 ARG A 393 *********************** 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 104 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.5941 (mpp) cc_final: 0.5613 (mpp) REVERT: H 160 TYR cc_start: 0.3310 (p90) cc_final: 0.2720 (p90) REVERT: A 71 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6368 (pt0) REVERT: A 471 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7514 (ptm160) REVERT: A 542 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7539 (m-30) outliers start: 17 outliers final: 8 residues processed: 101 average time/residue: 1.3180 time to fit residues: 142.8740 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** 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: 0.8030 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9854 Z= 0.199 Angle : 0.588 15.294 13392 Z= 0.306 Chirality : 0.044 0.206 1501 Planarity : 0.004 0.049 1687 Dihedral : 4.627 58.562 1330 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.10 % Favored : 94.65 % Rotamer: Outliers : 1.33 % Allowed : 13.77 % Favored : 84.90 % 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: 0.34 (0.25), residues: 1219 helix: 1.52 (0.25), residues: 454 sheet: 0.77 (0.34), residues: 255 loop : -1.30 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 110 HIS 0.004 0.001 HIS A 479 PHE 0.011 0.001 PHE A 348 TYR 0.016 0.001 TYR A 319 ARG 0.006 0.000 ARG A 393 *********************** 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 106 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6047 (mpp) cc_final: 0.5708 (mpp) REVERT: H 160 TYR cc_start: 0.3356 (p90) cc_final: 0.2767 (p90) REVERT: L 38 GLN cc_start: 0.5425 (tt0) cc_final: 0.5132 (tt0) REVERT: L 182 LEU cc_start: 0.4640 (mp) cc_final: 0.4223 (tp) REVERT: A 71 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6173 (pt0) REVERT: A 542 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7477 (m-30) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 1.2590 time to fit residues: 138.5294 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** 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: 0.8027 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9854 Z= 0.202 Angle : 0.581 15.088 13392 Z= 0.303 Chirality : 0.044 0.196 1501 Planarity : 0.004 0.048 1687 Dihedral : 4.644 59.950 1330 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 1.52 % Allowed : 13.49 % Favored : 85.00 % 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: 0.40 (0.25), residues: 1219 helix: 1.55 (0.25), residues: 462 sheet: 0.81 (0.34), residues: 253 loop : -1.28 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 110 HIS 0.003 0.001 HIS A 391 PHE 0.012 0.001 PHE A 320 TYR 0.017 0.001 TYR H 63 ARG 0.004 0.000 ARG A 393 *********************** 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 106 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6024 (mpp) cc_final: 0.5817 (mpp) REVERT: H 160 TYR cc_start: 0.3331 (p90) cc_final: 0.2730 (p90) REVERT: L 38 GLN cc_start: 0.5420 (tt0) cc_final: 0.5056 (tt0) REVERT: L 182 LEU cc_start: 0.4475 (mp) cc_final: 0.4054 (tt) REVERT: A 71 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6213 (pt0) REVERT: A 542 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: P 2 LYS cc_start: 0.7867 (pptt) cc_final: 0.7579 (pptt) outliers start: 16 outliers final: 6 residues processed: 103 average time/residue: 1.2127 time to fit residues: 134.5450 Evaluate side-chains 96 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** 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: 0.8027 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9854 Z= 0.204 Angle : 0.577 14.936 13392 Z= 0.301 Chirality : 0.044 0.189 1501 Planarity : 0.004 0.048 1687 Dihedral : 4.595 59.227 1330 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.16 % Rotamer: Outliers : 1.23 % Allowed : 14.34 % Favored : 84.43 % 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: 0.42 (0.25), residues: 1219 helix: 1.58 (0.25), residues: 462 sheet: 0.82 (0.34), residues: 253 loop : -1.28 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 110 HIS 0.004 0.001 HIS A 391 PHE 0.012 0.001 PHE A 320 TYR 0.016 0.001 TYR H 63 ARG 0.004 0.000 ARG A 393 *********************** 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 102 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6012 (mpp) cc_final: 0.5780 (mpp) REVERT: H 160 TYR cc_start: 0.3318 (p90) cc_final: 0.2810 (p90) REVERT: L 38 GLN cc_start: 0.5425 (tt0) cc_final: 0.5058 (tt0) REVERT: A 71 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6210 (pt0) REVERT: A 542 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7468 (m-30) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 1.1986 time to fit residues: 127.9615 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 98 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9854 Z= 0.198 Angle : 0.576 14.270 13392 Z= 0.299 Chirality : 0.044 0.172 1501 Planarity : 0.004 0.049 1687 Dihedral : 4.552 58.945 1330 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 1.04 % Allowed : 14.62 % Favored : 84.33 % 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: 0.45 (0.25), residues: 1219 helix: 1.61 (0.25), residues: 462 sheet: 0.81 (0.34), residues: 253 loop : -1.26 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 110 HIS 0.004 0.001 HIS A 391 PHE 0.012 0.001 PHE A 320 TYR 0.017 0.001 TYR H 63 ARG 0.004 0.000 ARG A 393 *********************** 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 100 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 TYR cc_start: 0.7068 (m-80) cc_final: 0.6846 (m-10) REVERT: H 160 TYR cc_start: 0.3316 (p90) cc_final: 0.2812 (p90) REVERT: L 38 GLN cc_start: 0.5420 (tt0) cc_final: 0.5124 (tt0) REVERT: A 71 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6199 (pt0) REVERT: A 542 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: A 561 MET cc_start: 0.8714 (mmp) cc_final: 0.8454 (mmp) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 1.2442 time to fit residues: 129.8830 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR 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: 0.9990 chunk 120 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9854 Z= 0.270 Angle : 0.627 15.094 13392 Z= 0.325 Chirality : 0.046 0.195 1501 Planarity : 0.005 0.051 1687 Dihedral : 4.698 57.536 1330 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 1.14 % Allowed : 14.53 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1219 helix: 1.48 (0.25), residues: 455 sheet: 0.80 (0.34), residues: 241 loop : -1.25 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 110 HIS 0.005 0.001 HIS A 391 PHE 0.014 0.002 PHE A 320 TYR 0.016 0.002 TYR A 319 ARG 0.005 0.000 ARG A 393 ********************** 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 95 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3168 (p90) cc_final: 0.2736 (p90) REVERT: L 38 GLN cc_start: 0.5363 (tt0) cc_final: 0.5070 (tt0) REVERT: A 71 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6212 (pt0) REVERT: A 542 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7501 (m-30) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 1.2716 time to fit residues: 127.3144 Evaluate side-chains 93 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 84 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 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 = 0.4329 r_free = 0.4329 target = 0.206841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109128 restraints weight = 15464.069| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.37 r_work: 0.2969 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9854 Z= 0.387 Angle : 0.697 15.888 13392 Z= 0.365 Chirality : 0.049 0.217 1501 Planarity : 0.005 0.067 1687 Dihedral : 4.990 56.312 1330 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.09 % Favored : 93.67 % Rotamer: Outliers : 1.04 % Allowed : 14.72 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.06 (0.24), residues: 1219 helix: 1.19 (0.25), residues: 454 sheet: 0.70 (0.34), residues: 240 loop : -1.34 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 110 HIS 0.007 0.002 HIS A 391 PHE 0.017 0.002 PHE A 224 TYR 0.018 0.002 TYR A 319 ARG 0.006 0.001 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3836.38 seconds wall clock time: 69 minutes 18.17 seconds (4158.17 seconds total)