Starting phenix.real_space_refine on Wed May 8 23:22:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/05_2024/8jpj_36481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/05_2024/8jpj_36481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/05_2024/8jpj_36481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/05_2024/8jpj_36481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/05_2024/8jpj_36481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpj_36481/05_2024/8jpj_36481.pdb" } resolution = 3.5 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= 0.005 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 70 5.16 5 Cl 4 4.86 5 C 7436 2.51 5 N 1914 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B GLU 762": "OE1" <-> "OE2" Residue "B GLU 779": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11448 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5722 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5722 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.60, per 1000 atoms: 0.58 Number of scatterers: 11448 At special positions: 0 Unit cell: (106.35, 82.9026, 116.399, 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) Cl 4 17.00 S 70 16.00 O 2024 8.00 N 1914 7.00 C 7436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 430 " 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: 4.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 65.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 69 through 124 removed outlier: 3.646A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 151 removed outlier: 3.932A pdb=" N LEU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.077A pdb=" N CYS A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.882A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 removed outlier: 4.239A pdb=" N HIS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.591A pdb=" N GLN A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 276 through 299 removed outlier: 3.850A pdb=" N PHE A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 333 through 365 Processing helix chain 'A' and resid 375 through 395 removed outlier: 3.570A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 444 removed outlier: 3.553A pdb=" N ASN A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 488 through 511 removed outlier: 3.945A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.135A pdb=" N ALA A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.654A pdb=" N ILE A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.679A pdb=" N LEU A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.788A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 773 through 780 removed outlier: 4.288A pdb=" N ASP A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 830 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 69 through 124 removed outlier: 3.647A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 151 removed outlier: 3.933A pdb=" N LEU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.077A pdb=" N CYS B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.882A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 218 removed outlier: 4.239A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Proline residue: B 215 - end of helix removed outlier: 3.591A pdb=" N GLN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.851A pdb=" N PHE B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 333 through 365 Processing helix chain 'B' and resid 375 through 395 removed outlier: 3.571A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 444 removed outlier: 3.552A pdb=" N ASN B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'B' and resid 461 through 480 Processing helix chain 'B' and resid 488 through 511 removed outlier: 3.946A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 534 removed outlier: 4.134A pdb=" N ALA B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.655A pdb=" N ILE B 557 " --> pdb=" O TYR B 553 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 560 " --> pdb=" O PRO B 556 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 582 Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.679A pdb=" N LEU B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.789A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 773 through 780 removed outlier: 4.288A pdb=" N ASP B 780 " --> pdb=" O GLU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 830 Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 854 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.482A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838 Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 401 Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.482A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838 670 hydrogen bonds defined for protein. 1980 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: 3.58 Time building geometry restraints manager: 4.62 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: 3613 1.34 - 1.46: 2834 1.46 - 1.58: 5151 1.58 - 1.70: 0 1.70 - 1.82: 110 Bond restraints: 11708 Sorted by residual: bond pdb=" CA VAL A 758 " pdb=" CB VAL A 758 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.35e+00 bond pdb=" CA VAL B 758 " pdb=" CB VAL B 758 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.28e+00 bond pdb=" N PRO B 368 " pdb=" CA PRO B 368 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.21e+00 bond pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.51e-01 bond pdb=" CA ILE B 159 " pdb=" C ILE B 159 " ideal model delta sigma weight residual 1.520 1.528 -0.008 8.80e-03 1.29e+04 8.53e-01 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.02: 258 106.02 - 113.01: 6365 113.01 - 120.00: 4035 120.00 - 127.00: 5094 127.00 - 133.99: 126 Bond angle restraints: 15878 Sorted by residual: angle pdb=" N VAL B 375 " pdb=" CA VAL B 375 " pdb=" C VAL B 375 " ideal model delta sigma weight residual 112.96 107.81 5.15 1.00e+00 1.00e+00 2.65e+01 angle pdb=" N VAL A 375 " pdb=" CA VAL A 375 " pdb=" C VAL A 375 " ideal model delta sigma weight residual 112.96 107.83 5.13 1.00e+00 1.00e+00 2.64e+01 angle pdb=" N VAL B 175 " pdb=" CA VAL B 175 " pdb=" C VAL B 175 " ideal model delta sigma weight residual 113.71 109.48 4.23 9.50e-01 1.11e+00 1.99e+01 angle pdb=" N VAL A 175 " pdb=" CA VAL A 175 " pdb=" C VAL A 175 " ideal model delta sigma weight residual 113.71 109.55 4.16 9.50e-01 1.11e+00 1.92e+01 angle pdb=" C GLY A 158 " pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 120.24 122.83 -2.59 6.30e-01 2.52e+00 1.69e+01 ... (remaining 15873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6253 17.54 - 35.08: 521 35.08 - 52.62: 96 52.62 - 70.16: 12 70.16 - 87.70: 14 Dihedral angle restraints: 6896 sinusoidal: 2698 harmonic: 4198 Sorted by residual: dihedral pdb=" CB CYS B 399 " pdb=" SG CYS B 399 " pdb=" SG CYS B 430 " pdb=" CB CYS B 430 " ideal model delta sinusoidal sigma weight residual 93.00 -179.30 -87.70 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 399 " pdb=" SG CYS A 399 " pdb=" SG CYS A 430 " pdb=" CB CYS A 430 " ideal model delta sinusoidal sigma weight residual 93.00 -179.31 -87.69 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual -86.00 -159.98 73.98 1 1.00e+01 1.00e-02 6.95e+01 ... (remaining 6893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1144 0.029 - 0.058: 452 0.058 - 0.088: 139 0.088 - 0.117: 83 0.117 - 0.146: 16 Chirality restraints: 1834 Sorted by residual: chirality pdb=" CB THR A 427 " pdb=" CA THR A 427 " pdb=" OG1 THR A 427 " pdb=" CG2 THR A 427 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CB THR B 427 " pdb=" CA THR B 427 " pdb=" OG1 THR B 427 " pdb=" CG2 THR B 427 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE A 847 " pdb=" N ILE A 847 " pdb=" C ILE A 847 " pdb=" CB ILE A 847 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1831 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 369 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 370 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 369 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO A 370 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 769 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 770 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 770 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 770 " -0.021 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2875 2.80 - 3.33: 11376 3.33 - 3.85: 17984 3.85 - 4.38: 19763 4.38 - 4.90: 35939 Nonbonded interactions: 87937 Sorted by model distance: nonbonded pdb=" ND2 ASN B 137 " pdb=" OG1 THR B 386 " model vdw 2.279 2.520 nonbonded pdb=" ND2 ASN A 137 " pdb=" OG1 THR A 386 " model vdw 2.279 2.520 nonbonded pdb=" O ILE B 624 " pdb=" OG1 THR B 628 " model vdw 2.293 2.440 nonbonded pdb=" O ILE A 624 " pdb=" OG1 THR A 628 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR B 520 " pdb=" OH TYR B 553 " model vdw 2.317 2.440 ... (remaining 87932 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 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 7.340 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.650 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 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 : 0.003 0.025 11708 Z= 0.208 Angle : 0.575 7.608 15878 Z= 0.325 Chirality : 0.039 0.146 1834 Planarity : 0.004 0.037 1994 Dihedral : 13.482 83.984 4182 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 1.48 (0.23), residues: 1446 helix: 2.20 (0.18), residues: 892 sheet: -1.52 (1.08), residues: 24 loop : -1.08 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 303 HIS 0.002 0.000 HIS A 515 PHE 0.012 0.001 PHE B 101 TYR 0.012 0.001 TYR A 866 ARG 0.003 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6371 (pt0) REVERT: A 71 LYS cc_start: 0.5897 (mmtt) cc_final: 0.5676 (mttp) REVERT: A 75 ARG cc_start: 0.6007 (ttt90) cc_final: 0.5357 (tpt170) REVERT: A 82 MET cc_start: 0.6724 (mtt) cc_final: 0.6399 (mtt) REVERT: A 200 GLU cc_start: 0.6712 (mp0) cc_final: 0.5364 (mp0) REVERT: A 589 GLU cc_start: 0.6415 (pt0) cc_final: 0.5722 (pm20) REVERT: A 611 TYR cc_start: 0.6042 (p90) cc_final: 0.5560 (p90) REVERT: A 822 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6335 (mt0) REVERT: A 843 GLU cc_start: 0.5157 (tt0) cc_final: 0.4747 (tm-30) REVERT: A 844 ILE cc_start: 0.6251 (tt) cc_final: 0.5831 (tt) REVERT: A 855 TYR cc_start: 0.7427 (t80) cc_final: 0.6911 (t80) REVERT: B 63 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6370 (pt0) REVERT: B 71 LYS cc_start: 0.5899 (mmtt) cc_final: 0.5676 (mttp) REVERT: B 75 ARG cc_start: 0.6013 (ttt90) cc_final: 0.5360 (tpt170) REVERT: B 82 MET cc_start: 0.6721 (mtt) cc_final: 0.6394 (mtt) REVERT: B 200 GLU cc_start: 0.6696 (mp0) cc_final: 0.5348 (mp0) REVERT: B 589 GLU cc_start: 0.6405 (pt0) cc_final: 0.5716 (pm20) REVERT: B 611 TYR cc_start: 0.6094 (p90) cc_final: 0.5605 (p90) REVERT: B 822 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6337 (mt0) REVERT: B 843 GLU cc_start: 0.5203 (tt0) cc_final: 0.4748 (tm-30) REVERT: B 844 ILE cc_start: 0.6289 (tt) cc_final: 0.5874 (tt) REVERT: B 855 TYR cc_start: 0.7431 (t80) cc_final: 0.6885 (t80) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2982 time to fit residues: 132.0404 Evaluate side-chains 168 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 132 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 355 ASN A 819 HIS A 859 GLN B 167 ASN B 819 HIS B 852 ASN B 859 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11708 Z= 0.276 Angle : 0.653 9.032 15878 Z= 0.336 Chirality : 0.044 0.149 1834 Planarity : 0.005 0.044 1994 Dihedral : 4.462 19.516 1574 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Rotamer: Outliers : 1.83 % Allowed : 12.10 % Favored : 86.07 % 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: 1.25 (0.22), residues: 1446 helix: 1.85 (0.17), residues: 908 sheet: -3.00 (0.88), residues: 24 loop : -0.85 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 272 HIS 0.009 0.002 HIS B 515 PHE 0.031 0.002 PHE A 473 TYR 0.017 0.002 TYR B 806 ARG 0.005 0.001 ARG B 861 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6316 (pt0) REVERT: A 71 LYS cc_start: 0.6096 (mttt) cc_final: 0.5814 (mttp) REVERT: A 82 MET cc_start: 0.7065 (mtt) cc_final: 0.6687 (mtt) REVERT: A 161 GLU cc_start: 0.6728 (mp0) cc_final: 0.5988 (mp0) REVERT: A 239 ARG cc_start: 0.7182 (ttt-90) cc_final: 0.6940 (ttt180) REVERT: A 313 ASN cc_start: 0.7841 (p0) cc_final: 0.7488 (p0) REVERT: A 360 LYS cc_start: 0.6494 (mttt) cc_final: 0.6204 (mtmt) REVERT: A 361 TYR cc_start: 0.7773 (t80) cc_final: 0.7557 (t80) REVERT: A 573 LYS cc_start: 0.7679 (mttt) cc_final: 0.7003 (mtmm) REVERT: A 587 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7355 (mp) REVERT: A 589 GLU cc_start: 0.6356 (pt0) cc_final: 0.5716 (pm20) REVERT: A 737 ARG cc_start: 0.6435 (ptp90) cc_final: 0.5852 (ptp90) REVERT: A 822 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6466 (mt0) REVERT: B 63 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6310 (pt0) REVERT: B 71 LYS cc_start: 0.6100 (mttt) cc_final: 0.5817 (mttp) REVERT: B 82 MET cc_start: 0.7062 (mtt) cc_final: 0.6692 (mtt) REVERT: B 161 GLU cc_start: 0.6722 (mp0) cc_final: 0.6002 (mp0) REVERT: B 203 MET cc_start: 0.7690 (mmm) cc_final: 0.7483 (tpp) REVERT: B 239 ARG cc_start: 0.7186 (ttt-90) cc_final: 0.6941 (ttt180) REVERT: B 313 ASN cc_start: 0.7843 (p0) cc_final: 0.7478 (p0) REVERT: B 360 LYS cc_start: 0.6493 (mttt) cc_final: 0.6188 (mtmt) REVERT: B 361 TYR cc_start: 0.7785 (t80) cc_final: 0.7556 (t80) REVERT: B 573 LYS cc_start: 0.7673 (mttt) cc_final: 0.7000 (mtmm) REVERT: B 587 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7363 (mp) REVERT: B 589 GLU cc_start: 0.6357 (pt0) cc_final: 0.5713 (pm20) REVERT: B 737 ARG cc_start: 0.6389 (ptp90) cc_final: 0.5840 (ptp90) REVERT: B 822 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6460 (mt0) outliers start: 23 outliers final: 9 residues processed: 201 average time/residue: 0.2999 time to fit residues: 81.3318 Evaluate side-chains 169 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 143 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN B 355 ASN B 456 GLN B 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11708 Z= 0.188 Angle : 0.536 13.533 15878 Z= 0.269 Chirality : 0.039 0.156 1834 Planarity : 0.004 0.041 1994 Dihedral : 4.056 20.230 1574 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.63 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 12.26 % Favored : 85.35 % 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 (0.22), residues: 1446 helix: 2.23 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.006 0.001 HIS B 865 PHE 0.017 0.001 PHE A 473 TYR 0.010 0.001 TYR B 613 ARG 0.002 0.000 ARG B 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6310 (pt0) REVERT: A 71 LYS cc_start: 0.5917 (mttt) cc_final: 0.5676 (mttp) REVERT: A 82 MET cc_start: 0.7105 (mtt) cc_final: 0.6726 (mtt) REVERT: A 119 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4764 (mp0) REVERT: A 161 GLU cc_start: 0.6938 (mp0) cc_final: 0.5827 (mp0) REVERT: A 239 ARG cc_start: 0.7054 (ttt-90) cc_final: 0.6827 (ttt180) REVERT: A 313 ASN cc_start: 0.7932 (p0) cc_final: 0.7657 (p0) REVERT: A 360 LYS cc_start: 0.6578 (mttt) cc_final: 0.6159 (mtmm) REVERT: A 361 TYR cc_start: 0.7798 (t80) cc_final: 0.7505 (t80) REVERT: A 573 LYS cc_start: 0.7686 (mttt) cc_final: 0.6993 (mtmm) REVERT: A 587 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7517 (mp) REVERT: A 589 GLU cc_start: 0.6376 (pt0) cc_final: 0.5798 (pm20) REVERT: A 737 ARG cc_start: 0.6753 (ptp90) cc_final: 0.6132 (ptp90) REVERT: A 799 MET cc_start: 0.7003 (tpp) cc_final: 0.6752 (tpt) REVERT: A 822 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6435 (mt0) REVERT: B 63 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6312 (pt0) REVERT: B 71 LYS cc_start: 0.5918 (mttt) cc_final: 0.5679 (mttp) REVERT: B 82 MET cc_start: 0.7107 (mtt) cc_final: 0.6731 (mtt) REVERT: B 119 GLU cc_start: 0.5161 (OUTLIER) cc_final: 0.4767 (mp0) REVERT: B 161 GLU cc_start: 0.6957 (mp0) cc_final: 0.5838 (mp0) REVERT: B 239 ARG cc_start: 0.7057 (ttt-90) cc_final: 0.6829 (ttt180) REVERT: B 313 ASN cc_start: 0.7878 (p0) cc_final: 0.7553 (p0) REVERT: B 360 LYS cc_start: 0.6584 (mttt) cc_final: 0.6186 (mtmm) REVERT: B 361 TYR cc_start: 0.7793 (t80) cc_final: 0.7508 (t80) REVERT: B 573 LYS cc_start: 0.7697 (mttt) cc_final: 0.7041 (mtmm) REVERT: B 587 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 589 GLU cc_start: 0.6373 (pt0) cc_final: 0.5801 (pm20) REVERT: B 822 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6429 (mt0) outliers start: 30 outliers final: 16 residues processed: 165 average time/residue: 0.2837 time to fit residues: 64.3992 Evaluate side-chains 159 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 742 HIS B 742 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11708 Z= 0.234 Angle : 0.562 11.486 15878 Z= 0.282 Chirality : 0.040 0.138 1834 Planarity : 0.004 0.044 1994 Dihedral : 4.075 19.184 1574 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.90 % Favored : 96.96 % Rotamer: Outliers : 2.63 % Allowed : 13.14 % Favored : 84.24 % 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: 1.57 (0.22), residues: 1446 helix: 2.20 (0.17), residues: 906 sheet: -3.12 (0.89), residues: 24 loop : -0.89 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 278 HIS 0.007 0.001 HIS B 865 PHE 0.019 0.001 PHE A 473 TYR 0.011 0.001 TYR B 613 ARG 0.004 0.000 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6449 (pt0) REVERT: A 71 LYS cc_start: 0.5995 (mttt) cc_final: 0.5727 (mttp) REVERT: A 82 MET cc_start: 0.7186 (mtt) cc_final: 0.6826 (mtt) REVERT: A 119 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4848 (mp0) REVERT: A 161 GLU cc_start: 0.7302 (mp0) cc_final: 0.6829 (mp0) REVERT: A 239 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6813 (ttt180) REVERT: A 313 ASN cc_start: 0.7962 (p0) cc_final: 0.7714 (p0) REVERT: A 360 LYS cc_start: 0.6604 (mttt) cc_final: 0.6214 (mtmm) REVERT: A 361 TYR cc_start: 0.7792 (t80) cc_final: 0.7440 (t80) REVERT: A 573 LYS cc_start: 0.7858 (mttt) cc_final: 0.6564 (mmtm) REVERT: A 587 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 589 GLU cc_start: 0.6319 (pt0) cc_final: 0.5777 (pm20) REVERT: A 822 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6413 (mt0) REVERT: B 63 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6450 (pt0) REVERT: B 71 LYS cc_start: 0.5994 (mttt) cc_final: 0.5728 (mttp) REVERT: B 82 MET cc_start: 0.7186 (mtt) cc_final: 0.6830 (mtt) REVERT: B 119 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4825 (mp0) REVERT: B 161 GLU cc_start: 0.7301 (mp0) cc_final: 0.6827 (mp0) REVERT: B 239 ARG cc_start: 0.7070 (ttt-90) cc_final: 0.6823 (ttt180) REVERT: B 313 ASN cc_start: 0.7923 (p0) cc_final: 0.7619 (p0) REVERT: B 360 LYS cc_start: 0.6602 (mttt) cc_final: 0.6215 (mtmm) REVERT: B 361 TYR cc_start: 0.7795 (t80) cc_final: 0.7445 (t80) REVERT: B 573 LYS cc_start: 0.7841 (mttt) cc_final: 0.6540 (mmtm) REVERT: B 587 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7542 (mp) REVERT: B 589 GLU cc_start: 0.6314 (pt0) cc_final: 0.5772 (pm20) REVERT: B 822 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6416 (mt0) outliers start: 33 outliers final: 23 residues processed: 156 average time/residue: 0.2687 time to fit residues: 58.1258 Evaluate side-chains 153 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11708 Z= 0.316 Angle : 0.636 13.089 15878 Z= 0.319 Chirality : 0.044 0.213 1834 Planarity : 0.005 0.047 1994 Dihedral : 4.472 21.294 1574 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Rotamer: Outliers : 2.79 % Allowed : 12.90 % Favored : 84.32 % 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: 1.22 (0.22), residues: 1446 helix: 1.90 (0.17), residues: 920 sheet: -3.05 (0.89), residues: 24 loop : -1.08 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 278 HIS 0.008 0.001 HIS B 865 PHE 0.024 0.002 PHE A 110 TYR 0.014 0.002 TYR A 613 ARG 0.003 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6464 (pt0) REVERT: A 71 LYS cc_start: 0.6157 (mttt) cc_final: 0.5791 (mttp) REVERT: A 82 MET cc_start: 0.7198 (mtt) cc_final: 0.6850 (mtt) REVERT: A 119 GLU cc_start: 0.5125 (OUTLIER) cc_final: 0.4635 (mp0) REVERT: A 161 GLU cc_start: 0.7438 (mp0) cc_final: 0.7154 (mp0) REVERT: A 239 ARG cc_start: 0.7049 (ttt-90) cc_final: 0.6743 (ttt180) REVERT: A 313 ASN cc_start: 0.7959 (p0) cc_final: 0.7712 (p0) REVERT: A 360 LYS cc_start: 0.6649 (mttt) cc_final: 0.6355 (mtmt) REVERT: A 361 TYR cc_start: 0.7732 (t80) cc_final: 0.7531 (t80) REVERT: A 573 LYS cc_start: 0.8013 (mttt) cc_final: 0.6812 (mmtm) REVERT: A 587 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7442 (mp) REVERT: A 589 GLU cc_start: 0.6339 (pt0) cc_final: 0.5803 (pm20) REVERT: A 822 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6403 (mt0) REVERT: B 63 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6438 (pt0) REVERT: B 71 LYS cc_start: 0.6155 (mttt) cc_final: 0.5792 (mttp) REVERT: B 82 MET cc_start: 0.7197 (mtt) cc_final: 0.6855 (mtt) REVERT: B 119 GLU cc_start: 0.5124 (OUTLIER) cc_final: 0.4631 (mp0) REVERT: B 161 GLU cc_start: 0.7438 (mp0) cc_final: 0.7152 (mp0) REVERT: B 239 ARG cc_start: 0.7051 (ttt-90) cc_final: 0.6745 (ttt180) REVERT: B 313 ASN cc_start: 0.7933 (p0) cc_final: 0.7629 (p0) REVERT: B 360 LYS cc_start: 0.6624 (mttt) cc_final: 0.6335 (mtmt) REVERT: B 428 PHE cc_start: 0.8048 (m-80) cc_final: 0.7782 (m-10) REVERT: B 444 ASN cc_start: 0.7668 (m-40) cc_final: 0.7383 (m-40) REVERT: B 573 LYS cc_start: 0.8048 (mttt) cc_final: 0.6860 (mmtm) REVERT: B 587 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7441 (mp) REVERT: B 589 GLU cc_start: 0.6335 (pt0) cc_final: 0.5799 (pm20) REVERT: B 822 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6399 (mt0) outliers start: 35 outliers final: 31 residues processed: 159 average time/residue: 0.2875 time to fit residues: 64.0811 Evaluate side-chains 161 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.0040 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11708 Z= 0.160 Angle : 0.512 9.753 15878 Z= 0.259 Chirality : 0.037 0.138 1834 Planarity : 0.004 0.046 1994 Dihedral : 4.094 21.616 1574 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.03 % Rotamer: Outliers : 1.91 % Allowed : 14.41 % Favored : 83.68 % 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: 1.52 (0.22), residues: 1446 helix: 2.22 (0.17), residues: 916 sheet: -3.32 (0.90), residues: 24 loop : -1.10 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 590 HIS 0.007 0.001 HIS A 865 PHE 0.015 0.001 PHE A 473 TYR 0.010 0.001 TYR B 613 ARG 0.003 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6376 (pt0) REVERT: A 71 LYS cc_start: 0.5974 (mttt) cc_final: 0.5723 (mttp) REVERT: A 82 MET cc_start: 0.7167 (mtt) cc_final: 0.6839 (mtt) REVERT: A 161 GLU cc_start: 0.7487 (mp0) cc_final: 0.7047 (mt-10) REVERT: A 239 ARG cc_start: 0.6856 (ttt-90) cc_final: 0.6506 (ttt180) REVERT: A 313 ASN cc_start: 0.7951 (p0) cc_final: 0.7726 (p0) REVERT: A 360 LYS cc_start: 0.6608 (mttt) cc_final: 0.6213 (mtmm) REVERT: A 361 TYR cc_start: 0.7758 (t80) cc_final: 0.7481 (t80) REVERT: A 573 LYS cc_start: 0.7901 (mttt) cc_final: 0.6651 (mmtm) REVERT: A 589 GLU cc_start: 0.6346 (pt0) cc_final: 0.5799 (pm20) REVERT: A 822 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6399 (mt0) REVERT: B 63 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6379 (pt0) REVERT: B 71 LYS cc_start: 0.5990 (mttt) cc_final: 0.5746 (mttp) REVERT: B 82 MET cc_start: 0.7163 (mtt) cc_final: 0.6841 (mtt) REVERT: B 161 GLU cc_start: 0.7488 (mp0) cc_final: 0.7046 (mt-10) REVERT: B 239 ARG cc_start: 0.6856 (ttt-90) cc_final: 0.6506 (ttt180) REVERT: B 313 ASN cc_start: 0.7908 (p0) cc_final: 0.7615 (p0) REVERT: B 360 LYS cc_start: 0.6597 (mttt) cc_final: 0.6200 (mtmm) REVERT: B 573 LYS cc_start: 0.7903 (mttt) cc_final: 0.6652 (mmtm) REVERT: B 589 GLU cc_start: 0.6338 (pt0) cc_final: 0.5794 (pm20) REVERT: B 822 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6400 (mt0) outliers start: 24 outliers final: 22 residues processed: 136 average time/residue: 0.2748 time to fit residues: 52.2954 Evaluate side-chains 142 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 140 optimal weight: 0.4980 chunk 88 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11708 Z= 0.154 Angle : 0.501 10.655 15878 Z= 0.252 Chirality : 0.037 0.138 1834 Planarity : 0.004 0.045 1994 Dihedral : 3.950 20.945 1574 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.04 % Favored : 96.82 % Rotamer: Outliers : 1.83 % Allowed : 15.21 % Favored : 82.96 % 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 (0.22), residues: 1446 helix: 2.38 (0.17), residues: 914 sheet: -3.30 (0.91), residues: 24 loop : -1.04 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 590 HIS 0.008 0.001 HIS B 865 PHE 0.015 0.001 PHE A 473 TYR 0.008 0.001 TYR A 613 ARG 0.002 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6328 (pt0) REVERT: A 71 LYS cc_start: 0.5954 (mttt) cc_final: 0.5724 (mttp) REVERT: A 82 MET cc_start: 0.7204 (mtt) cc_final: 0.6904 (mtt) REVERT: A 161 GLU cc_start: 0.7391 (mp0) cc_final: 0.6887 (mt-10) REVERT: A 239 ARG cc_start: 0.6936 (ttt-90) cc_final: 0.6533 (ttt180) REVERT: A 313 ASN cc_start: 0.7942 (p0) cc_final: 0.7737 (p0) REVERT: A 360 LYS cc_start: 0.6557 (mttt) cc_final: 0.6280 (mtmt) REVERT: A 361 TYR cc_start: 0.7764 (t80) cc_final: 0.7481 (t80) REVERT: A 573 LYS cc_start: 0.7907 (mttt) cc_final: 0.6614 (mmtm) REVERT: A 587 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7579 (mp) REVERT: A 589 GLU cc_start: 0.6364 (pt0) cc_final: 0.5819 (pm20) REVERT: A 822 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6378 (mt0) REVERT: B 63 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6330 (pt0) REVERT: B 71 LYS cc_start: 0.5963 (mttt) cc_final: 0.5743 (mttp) REVERT: B 82 MET cc_start: 0.7202 (mtt) cc_final: 0.6906 (mtt) REVERT: B 161 GLU cc_start: 0.7396 (mp0) cc_final: 0.6889 (mt-10) REVERT: B 239 ARG cc_start: 0.6937 (ttt-90) cc_final: 0.6536 (ttt180) REVERT: B 313 ASN cc_start: 0.7916 (p0) cc_final: 0.7646 (p0) REVERT: B 360 LYS cc_start: 0.6544 (mttt) cc_final: 0.6264 (mtmt) REVERT: B 573 LYS cc_start: 0.7886 (mttt) cc_final: 0.6625 (mmtm) REVERT: B 587 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7576 (mp) REVERT: B 589 GLU cc_start: 0.6355 (pt0) cc_final: 0.5813 (pm20) REVERT: B 822 GLN cc_start: 0.7018 (mm-40) cc_final: 0.6373 (mt0) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.2491 time to fit residues: 45.2865 Evaluate side-chains 136 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 849 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 84 optimal weight: 0.0770 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.6373 Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: