Starting phenix.real_space_refine on Sat Feb 17 16:44:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhn_31587/02_2024/7fhn_31587.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhn_31587/02_2024/7fhn_31587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhn_31587/02_2024/7fhn_31587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhn_31587/02_2024/7fhn_31587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhn_31587/02_2024/7fhn_31587.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fhn_31587/02_2024/7fhn_31587.pdb" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8728 atoms to isotropic. 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 Ca 6 9.91 5 S 44 5.16 5 C 7102 2.51 5 N 1630 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C ARG 543": "NH1" <-> "NH2" 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: 10648 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.62, per 1000 atoms: 0.53 Number of scatterers: 10648 At special positions: 0 Unit cell: (108.498, 119.652, 100.386, 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) Ca 6 19.99 S 44 16.00 O 1866 8.00 N 1630 7.00 C 7102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 101 " 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: 4.01 Conformation dependent library (CDL) restraints added in 1.8 seconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 80.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.601A pdb=" N ASP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.536A pdb=" N ILE A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 52' Processing helix chain 'A' and resid 56 through 69 removed outlier: 4.180A pdb=" N SER A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.582A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.652A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.759A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.874A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.681A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 335 removed outlier: 3.660A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.639A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 4.065A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.057A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.666A pdb=" N TYR A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.517A pdb=" N ARG A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 3.618A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.582A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 517 removed outlier: 3.900A pdb=" N THR A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 548 through 587 removed outlier: 3.622A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.712A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.565A pdb=" N GLY A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.857A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.937A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.972A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.624A pdb=" N ASP C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.695A pdb=" N LEU C 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 69 removed outlier: 4.040A pdb=" N SER C 60 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.506A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.582A pdb=" N TRP C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.681A pdb=" N ILE C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 238 removed outlier: 4.658A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.606A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 335 removed outlier: 4.381A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 365 through 376 removed outlier: 4.182A pdb=" N GLY C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 390 through 396 removed outlier: 4.140A pdb=" N ALA C 396 " --> pdb=" O CYS C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.606A pdb=" N TYR C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.526A pdb=" N ARG C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.710A pdb=" N TYR C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.706A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 4.637A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 516 removed outlier: 3.596A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 543 removed outlier: 3.576A pdb=" N ILE C 530 " --> pdb=" O ASN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 547 Processing helix chain 'C' and resid 548 through 565 Proline residue: C 563 - end of helix Processing helix chain 'C' and resid 565 through 587 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.711A pdb=" N GLU C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 628 removed outlier: 3.594A pdb=" N GLY C 619 " --> pdb=" O ASP C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.918A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 660 removed outlier: 3.919A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 684 removed outlier: 3.572A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU C 683 " --> pdb=" O LEU C 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA2, first strand: chain 'C' and resid 341 through 342 707 hydrogen bonds defined for protein. 2091 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: 2.89 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3189 1.34 - 1.46: 2356 1.46 - 1.57: 5317 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 10934 Sorted by residual: bond pdb=" CA ILE C 562 " pdb=" CB ILE C 562 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.54e+00 bond pdb=" CG LEU A 312 " pdb=" CD2 LEU A 312 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" C LEU A 109 " pdb=" N GLY A 110 " ideal model delta sigma weight residual 1.319 1.333 -0.014 1.34e-02 5.57e+03 1.10e+00 bond pdb=" CG LEU C 109 " pdb=" CD1 LEU C 109 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CG LEU A 115 " pdb=" CD1 LEU A 115 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.81e-01 ... (remaining 10929 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.67: 127 104.67 - 112.03: 5180 112.03 - 119.38: 3729 119.38 - 126.74: 5683 126.74 - 134.09: 157 Bond angle restraints: 14876 Sorted by residual: angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 110.66 118.61 -7.95 2.18e+00 2.10e-01 1.33e+01 angle pdb=" C PHE C 351 " pdb=" N GLU C 352 " pdb=" CA GLU C 352 " ideal model delta sigma weight residual 121.18 114.41 6.77 1.98e+00 2.55e-01 1.17e+01 angle pdb=" C VAL A 628 " pdb=" CA VAL A 628 " pdb=" CB VAL A 628 " ideal model delta sigma weight residual 110.93 107.24 3.69 1.10e+00 8.26e-01 1.13e+01 angle pdb=" N GLU C 352 " pdb=" CA GLU C 352 " pdb=" CB GLU C 352 " ideal model delta sigma weight residual 110.39 116.10 -5.71 1.75e+00 3.27e-01 1.06e+01 angle pdb=" C ILE C 542 " pdb=" CA ILE C 542 " pdb=" CB ILE C 542 " ideal model delta sigma weight residual 112.04 107.83 4.21 1.31e+00 5.83e-01 1.03e+01 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5660 17.18 - 34.35: 536 34.35 - 51.53: 90 51.53 - 68.71: 16 68.71 - 85.89: 10 Dihedral angle restraints: 6312 sinusoidal: 2484 harmonic: 3828 Sorted by residual: dihedral pdb=" CB CYS A 93 " pdb=" SG CYS A 93 " pdb=" SG CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sinusoidal sigma weight residual 93.00 137.62 -44.62 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " pdb=" SG CYS C 101 " pdb=" CB CYS C 101 " ideal model delta sinusoidal sigma weight residual 93.00 137.40 -44.40 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N PRO C 99 " pdb=" CA PRO C 99 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1067 0.034 - 0.068: 493 0.068 - 0.102: 91 0.102 - 0.136: 28 0.136 - 0.169: 7 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA LYS C 462 " pdb=" N LYS C 462 " pdb=" C LYS C 462 " pdb=" CB LYS C 462 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA LYS C 98 " pdb=" N LYS C 98 " pdb=" C LYS C 98 " pdb=" CB LYS C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA LYS A 462 " pdb=" N LYS A 462 " pdb=" C LYS A 462 " pdb=" CB LYS A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1683 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 293 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C VAL C 293 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL C 293 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR C 294 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 562 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO A 563 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 501 " -0.014 2.00e-02 2.50e+03 1.29e-02 2.93e+00 pdb=" CG PHE C 501 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 501 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 501 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 501 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 501 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 501 " -0.001 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 134 2.67 - 3.22: 10864 3.22 - 3.78: 17133 3.78 - 4.34: 21992 4.34 - 4.90: 36140 Nonbonded interactions: 86263 Sorted by model distance: nonbonded pdb=" O TRP C 647 " pdb=" OG1 THR C 650 " model vdw 2.107 2.440 nonbonded pdb=" OG SER C 265 " pdb=" OE1 GLN C 633 " model vdw 2.127 2.440 nonbonded pdb=" O TRP A 647 " pdb=" OG1 THR A 650 " model vdw 2.139 2.440 nonbonded pdb=" ND2 ASN C 339 " pdb="CA CA C1002 " model vdw 2.144 2.590 nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 633 " model vdw 2.158 2.440 ... (remaining 86258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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=1.00 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.000 Extract box with map and model: 3.360 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.570 Find NCS groups from input model: 0.530 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 0.049 10934 Z= 0.244 Angle : 0.648 7.952 14876 Z= 0.345 Chirality : 0.040 0.169 1686 Planarity : 0.004 0.044 1832 Dihedral : 13.868 85.886 3834 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.23), residues: 1282 helix: 1.62 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.001 0.000 HIS A 416 PHE 0.029 0.002 PHE C 501 TYR 0.020 0.002 TYR C 294 ARG 0.006 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7845 (mm-30) cc_final: 0.6678 (tm-30) REVERT: A 171 PHE cc_start: 0.7973 (t80) cc_final: 0.7772 (t80) REVERT: A 320 ASP cc_start: 0.8325 (m-30) cc_final: 0.8023 (t0) REVERT: A 392 CYS cc_start: 0.6847 (m) cc_final: 0.6531 (m) REVERT: A 670 PHE cc_start: 0.8228 (m-80) cc_final: 0.8022 (m-80) REVERT: C 111 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6777 (tm-30) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.2043 time to fit residues: 72.1542 Evaluate side-chains 172 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 HIS C 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10934 Z= 0.279 Angle : 0.639 8.117 14876 Z= 0.326 Chirality : 0.042 0.186 1686 Planarity : 0.004 0.042 1832 Dihedral : 4.139 21.879 1406 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.65 % Allowed : 10.05 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1282 helix: 1.76 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -0.62 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 271 HIS 0.002 0.001 HIS A 410 PHE 0.023 0.002 PHE A 499 TYR 0.020 0.002 TYR C 294 ARG 0.007 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7697 (mm-30) cc_final: 0.6646 (tm-30) REVERT: A 320 ASP cc_start: 0.8318 (m-30) cc_final: 0.8020 (t0) REVERT: A 670 PHE cc_start: 0.8129 (m-80) cc_final: 0.7927 (m-80) REVERT: C 111 GLU cc_start: 0.7717 (mm-30) cc_final: 0.6527 (tm-30) REVERT: C 258 MET cc_start: 0.7504 (mmm) cc_final: 0.6904 (mmm) REVERT: C 478 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8513 (tm-30) outliers start: 19 outliers final: 15 residues processed: 201 average time/residue: 0.1963 time to fit residues: 58.3139 Evaluate side-chains 186 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** C 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10934 Z= 0.186 Angle : 0.587 7.487 14876 Z= 0.298 Chirality : 0.040 0.192 1686 Planarity : 0.003 0.043 1832 Dihedral : 3.999 20.705 1406 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.39 % Allowed : 14.04 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1282 helix: 1.93 (0.17), residues: 946 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 271 HIS 0.004 0.001 HIS C 410 PHE 0.021 0.001 PHE C 444 TYR 0.016 0.001 TYR C 491 ARG 0.004 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6630 (tm-30) REVERT: A 212 MET cc_start: 0.6700 (mtm) cc_final: 0.6467 (mtp) REVERT: A 320 ASP cc_start: 0.8309 (m-30) cc_final: 0.8041 (t0) REVERT: A 670 PHE cc_start: 0.8069 (m-80) cc_final: 0.7840 (m-80) REVERT: C 111 GLU cc_start: 0.7756 (mm-30) cc_final: 0.6629 (tm-30) REVERT: C 258 MET cc_start: 0.7498 (mmm) cc_final: 0.6909 (mmm) REVERT: C 322 MET cc_start: 0.7252 (tmm) cc_final: 0.7049 (tmm) REVERT: C 478 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8565 (tm-30) outliers start: 16 outliers final: 12 residues processed: 213 average time/residue: 0.1868 time to fit residues: 59.5228 Evaluate side-chains 188 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10934 Z= 0.167 Angle : 0.558 6.956 14876 Z= 0.285 Chirality : 0.039 0.196 1686 Planarity : 0.003 0.054 1832 Dihedral : 3.864 19.769 1406 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.65 % Allowed : 16.03 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1282 helix: 2.01 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.32 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 PHE 0.024 0.001 PHE A 499 TYR 0.019 0.001 TYR C 491 ARG 0.003 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7791 (mm-30) cc_final: 0.6733 (tm-30) REVERT: A 212 MET cc_start: 0.6763 (mtm) cc_final: 0.6516 (mtp) REVERT: A 237 MET cc_start: 0.6773 (ttt) cc_final: 0.6535 (ttm) REVERT: A 320 ASP cc_start: 0.8308 (m-30) cc_final: 0.8036 (t0) REVERT: A 322 MET cc_start: 0.7909 (ppp) cc_final: 0.7513 (ppp) REVERT: C 111 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6534 (tm-30) REVERT: C 258 MET cc_start: 0.7625 (mmm) cc_final: 0.6994 (mmm) outliers start: 19 outliers final: 14 residues processed: 196 average time/residue: 0.1867 time to fit residues: 54.4395 Evaluate side-chains 187 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10934 Z= 0.228 Angle : 0.590 7.905 14876 Z= 0.298 Chirality : 0.040 0.166 1686 Planarity : 0.003 0.042 1832 Dihedral : 3.891 19.703 1406 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.25 % Allowed : 17.68 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1282 helix: 2.00 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -0.41 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 271 HIS 0.001 0.001 HIS C 134 PHE 0.022 0.001 PHE C 444 TYR 0.017 0.002 TYR C 491 ARG 0.002 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7729 (mm-30) cc_final: 0.6772 (tm-30) REVERT: A 212 MET cc_start: 0.6716 (mtm) cc_final: 0.6468 (mtp) REVERT: A 237 MET cc_start: 0.6925 (ttt) cc_final: 0.6677 (ttm) REVERT: A 320 ASP cc_start: 0.8337 (m-30) cc_final: 0.8035 (t0) REVERT: A 322 MET cc_start: 0.7990 (ppp) cc_final: 0.7597 (ppp) REVERT: A 579 TYR cc_start: 0.9007 (m-80) cc_final: 0.8731 (m-80) REVERT: A 597 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8137 (mmmt) REVERT: C 111 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6484 (tm-30) REVERT: C 258 MET cc_start: 0.7614 (mmm) cc_final: 0.6963 (mmm) REVERT: C 505 TRP cc_start: 0.8395 (OUTLIER) cc_final: 0.7823 (m100) REVERT: C 597 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8140 (mmmt) outliers start: 26 outliers final: 15 residues processed: 206 average time/residue: 0.2085 time to fit residues: 62.3670 Evaluate side-chains 194 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.0070 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10934 Z= 0.192 Angle : 0.568 7.155 14876 Z= 0.287 Chirality : 0.040 0.244 1686 Planarity : 0.003 0.043 1832 Dihedral : 3.831 18.178 1406 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.43 % Allowed : 18.37 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1282 helix: 2.02 (0.17), residues: 946 sheet: None (None), residues: 0 loop : -0.35 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 PHE 0.026 0.001 PHE C 351 TYR 0.013 0.001 TYR C 294 ARG 0.002 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6800 (tm-30) REVERT: A 237 MET cc_start: 0.7065 (ttt) cc_final: 0.6850 (ttm) REVERT: A 320 ASP cc_start: 0.8295 (m-30) cc_final: 0.7994 (t0) REVERT: A 322 MET cc_start: 0.8016 (ppp) cc_final: 0.7620 (ppp) REVERT: C 111 GLU cc_start: 0.7740 (mm-30) cc_final: 0.6507 (tm-30) REVERT: C 164 PHE cc_start: 0.8883 (t80) cc_final: 0.8634 (t80) REVERT: C 258 MET cc_start: 0.7636 (mmm) cc_final: 0.6998 (mmm) REVERT: C 505 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7716 (m100) outliers start: 28 outliers final: 18 residues processed: 213 average time/residue: 0.2017 time to fit residues: 62.9433 Evaluate side-chains 202 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10934 Z= 0.179 Angle : 0.582 12.551 14876 Z= 0.291 Chirality : 0.040 0.262 1686 Planarity : 0.003 0.043 1832 Dihedral : 3.774 17.799 1406 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.08 % Allowed : 19.06 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1282 helix: 2.07 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.21 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 PHE 0.029 0.001 PHE A 229 TYR 0.012 0.001 TYR A 532 ARG 0.003 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7834 (mm-30) cc_final: 0.6771 (tm-30) REVERT: A 319 MET cc_start: 0.6155 (tpp) cc_final: 0.5916 (tpt) REVERT: A 320 ASP cc_start: 0.8300 (m-30) cc_final: 0.7993 (t0) REVERT: A 505 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.7688 (m100) REVERT: A 678 GLU cc_start: 0.7397 (pp20) cc_final: 0.7121 (tm-30) REVERT: C 111 GLU cc_start: 0.7671 (mm-30) cc_final: 0.6418 (tm-30) REVERT: C 212 MET cc_start: 0.6607 (mtm) cc_final: 0.6392 (mtp) REVERT: C 258 MET cc_start: 0.7636 (mmm) cc_final: 0.7005 (mmm) REVERT: C 322 MET cc_start: 0.7379 (tmm) cc_final: 0.7097 (tmm) REVERT: C 505 TRP cc_start: 0.8297 (OUTLIER) cc_final: 0.7717 (m100) outliers start: 24 outliers final: 15 residues processed: 207 average time/residue: 0.1936 time to fit residues: 60.3098 Evaluate side-chains 202 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10934 Z= 0.201 Angle : 0.592 12.373 14876 Z= 0.296 Chirality : 0.041 0.274 1686 Planarity : 0.003 0.042 1832 Dihedral : 3.778 18.227 1406 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.73 % Allowed : 20.10 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.24), residues: 1282 helix: 2.05 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.21 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 PHE 0.028 0.001 PHE A 229 TYR 0.013 0.001 TYR C 294 ARG 0.003 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7855 (mm-30) cc_final: 0.6737 (tm-30) REVERT: A 319 MET cc_start: 0.6250 (tpp) cc_final: 0.5992 (tpt) REVERT: A 320 ASP cc_start: 0.8340 (m-30) cc_final: 0.8031 (t0) REVERT: A 488 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5666 (t80) REVERT: A 678 GLU cc_start: 0.7436 (pp20) cc_final: 0.7166 (tm-30) REVERT: C 111 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6608 (tm-30) REVERT: C 212 MET cc_start: 0.6618 (mtm) cc_final: 0.6392 (mtp) REVERT: C 258 MET cc_start: 0.7639 (mmm) cc_final: 0.7005 (mmm) REVERT: C 322 MET cc_start: 0.7427 (tmm) cc_final: 0.7132 (tmm) REVERT: C 453 LEU cc_start: 0.8574 (mm) cc_final: 0.8119 (tp) REVERT: C 505 TRP cc_start: 0.8240 (OUTLIER) cc_final: 0.7660 (m100) outliers start: 20 outliers final: 17 residues processed: 202 average time/residue: 0.1833 time to fit residues: 55.5587 Evaluate side-chains 201 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 488 PHE Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10934 Z= 0.188 Angle : 0.610 13.233 14876 Z= 0.298 Chirality : 0.041 0.340 1686 Planarity : 0.003 0.043 1832 Dihedral : 3.745 18.313 1406 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.65 % Allowed : 20.71 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.24), residues: 1282 helix: 2.07 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 464 HIS 0.002 0.001 HIS A 134 PHE 0.024 0.001 PHE C 195 TYR 0.014 0.001 TYR A 532 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7839 (mm-30) cc_final: 0.6713 (tm-30) REVERT: A 319 MET cc_start: 0.6266 (tpp) cc_final: 0.5999 (tpt) REVERT: A 320 ASP cc_start: 0.8297 (m-30) cc_final: 0.7996 (t0) REVERT: A 505 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7543 (m100) REVERT: A 678 GLU cc_start: 0.7384 (pp20) cc_final: 0.7102 (tm-30) REVERT: C 111 GLU cc_start: 0.7641 (mm-30) cc_final: 0.6430 (tm-30) REVERT: C 212 MET cc_start: 0.6752 (mtm) cc_final: 0.6532 (mtp) REVERT: C 258 MET cc_start: 0.7640 (mmm) cc_final: 0.7008 (mmm) REVERT: C 322 MET cc_start: 0.7433 (tmm) cc_final: 0.7123 (tmm) REVERT: C 505 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7639 (m100) outliers start: 19 outliers final: 16 residues processed: 200 average time/residue: 0.1789 time to fit residues: 54.4654 Evaluate side-chains 205 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10934 Z= 0.173 Angle : 0.604 14.450 14876 Z= 0.294 Chirality : 0.041 0.380 1686 Planarity : 0.003 0.043 1832 Dihedral : 3.692 17.984 1406 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.73 % Allowed : 20.97 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.24), residues: 1282 helix: 2.11 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.14 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 PHE 0.026 0.001 PHE C 501 TYR 0.014 0.001 TYR A 532 ARG 0.004 0.000 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7819 (mm-30) cc_final: 0.6710 (tm-30) REVERT: A 319 MET cc_start: 0.6270 (tpp) cc_final: 0.5996 (tpt) REVERT: A 320 ASP cc_start: 0.8344 (m-30) cc_final: 0.8036 (t0) REVERT: A 479 MET cc_start: 0.7338 (ppp) cc_final: 0.7042 (ppp) REVERT: A 486 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: A 505 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7490 (m100) REVERT: A 678 GLU cc_start: 0.7329 (pp20) cc_final: 0.7031 (tm-30) REVERT: C 111 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6457 (tm-30) REVERT: C 212 MET cc_start: 0.6748 (mtm) cc_final: 0.6507 (mtp) REVERT: C 258 MET cc_start: 0.7637 (mmm) cc_final: 0.7006 (mmm) REVERT: C 322 MET cc_start: 0.7433 (tmm) cc_final: 0.7105 (tmm) REVERT: C 505 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7683 (m100) REVERT: C 579 TYR cc_start: 0.9035 (m-80) cc_final: 0.8718 (m-80) outliers start: 20 outliers final: 16 residues processed: 198 average time/residue: 0.1815 time to fit residues: 54.0237 Evaluate side-chains 200 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** 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 = 0.4148 r_free = 0.4148 target = 0.153287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.119054 restraints weight = 18389.991| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.16 r_work: 0.3462 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10934 Z= 0.163 Angle : 0.604 15.004 14876 Z= 0.292 Chirality : 0.041 0.386 1686 Planarity : 0.003 0.043 1832 Dihedral : 3.625 16.202 1406 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.73 % Allowed : 21.06 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.24), residues: 1282 helix: 2.19 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.09 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 PHE 0.027 0.001 PHE C 351 TYR 0.014 0.001 TYR A 532 ARG 0.005 0.000 ARG C 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.96 seconds wall clock time: 45 minutes 3.94 seconds (2703.94 seconds total)