Starting phenix.real_space_refine on Wed Jun 26 05:13:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yr4_39535/06_2024/8yr4_39535_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 Cd 1 9.23 5 S 38 5.16 5 C 5982 2.51 5 N 1612 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 295": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 2": not complete - not flipped Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9323 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4628 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 572} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4628 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 572} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Classifications: {'peptide': 2} Modifications used: {'COO': 1} Link IDs: {'TRANS': 1} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Classifications: {'peptide': 2} Link IDs: {'CIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Classifications: {'peptide': 2} Modifications used: {'COO': 1} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Ad-hoc single atom residues: {' CD': 1} Classifications: {'peptide': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'FGA:plan-1': 1, 'FGA:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'FGA:plan-1': 1, 'FGA:plan-2': 1} Unresolved non-hydrogen planarities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9301 SG CYS J 1 48.228 39.651 56.391 1.00201.68 S Time building chain proxies: 5.69, per 1000 atoms: 0.61 Number of scatterers: 9323 At special positions: 0 Unit cell: (100.43, 83.83, 137.78, 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) Cd 1 47.96 S 38 16.00 O 1690 8.00 N 1612 7.00 C 5982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB FGA F 101 " pdb=" CB FGA I 101 " Number of C-beta restraints generated: 2168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 6 sheets defined 64.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 259 through 295 removed outlier: 3.576A pdb=" N LEU A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.500A pdb=" N GLU A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 328 through 353 removed outlier: 4.159A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.502A pdb=" N ILE A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 458 removed outlier: 3.912A pdb=" N TRP A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 469 through 521 Processing helix chain 'A' and resid 527 through 568 removed outlier: 4.083A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 5.064A pdb=" N TRP A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 680 through 687 removed outlier: 4.424A pdb=" N GLY A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 759 through 773 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.814A pdb=" N ASN A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 259 through 295 removed outlier: 3.595A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.525A pdb=" N GLU B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 Processing helix chain 'B' and resid 328 through 353 removed outlier: 4.119A pdb=" N PHE B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 366 through 390 removed outlier: 3.512A pdb=" N ALA B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.524A pdb=" N ILE B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 458 removed outlier: 3.924A pdb=" N TRP B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 469 through 521 Processing helix chain 'B' and resid 527 through 568 removed outlier: 4.103A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Proline residue: B 543 - end of helix removed outlier: 5.033A pdb=" N TRP B 546 " --> pdb=" O MET B 542 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLY B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 549 " --> pdb=" O ASN B 545 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 654 through 656 No H-bonds generated for 'chain 'B' and resid 654 through 656' Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'B' and resid 680 through 687 removed outlier: 4.434A pdb=" N GLY B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 759 through 773 Processing helix chain 'B' and resid 785 through 790 removed outlier: 3.775A pdb=" N ASN B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 817 through 824 Processing sheet with id= A, first strand: chain 'A' and resid 590 through 593 Processing sheet with id= B, first strand: chain 'A' and resid 778 through 781 removed outlier: 6.439A pdb=" N GLN A 793 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A 622 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 795 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 806 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 804 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 666 through 669 removed outlier: 6.370A pdb=" N ILE A 747 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 669 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 749 " --> pdb=" O VAL A 669 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 590 through 593 Processing sheet with id= E, first strand: chain 'B' and resid 778 through 781 removed outlier: 6.466A pdb=" N GLN B 793 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL B 622 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 795 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 806 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 804 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 666 through 669 removed outlier: 6.089A pdb=" N ILE B 747 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL B 669 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU B 749 " --> pdb=" O VAL B 669 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 557 hydrogen bonds defined for protein. 1665 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: 2.41 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3052 1.35 - 1.47: 2285 1.47 - 1.59: 4099 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 9496 Sorted by residual: bond pdb=" CD FGA I 101 " pdb=" OE1 FGA I 101 " ideal model delta sigma weight residual 1.259 1.225 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" CD FGA F 101 " pdb=" OE1 FGA F 101 " ideal model delta sigma weight residual 1.259 1.225 0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" N GLY H 2 " pdb=" CA GLY H 2 " ideal model delta sigma weight residual 1.451 1.476 -0.025 1.60e-02 3.91e+03 2.43e+00 bond pdb=" N CYS I 1 " pdb=" CA CYS I 1 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.94e+00 bond pdb=" N CYS J 1 " pdb=" CA CYS J 1 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.84e+00 ... (remaining 9491 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.73: 146 106.73 - 113.55: 5323 113.55 - 120.38: 3651 120.38 - 127.21: 3664 127.21 - 134.04: 82 Bond angle restraints: 12866 Sorted by residual: angle pdb=" CA TRP A 434 " pdb=" CB TRP A 434 " pdb=" CG TRP A 434 " ideal model delta sigma weight residual 113.60 119.95 -6.35 1.90e+00 2.77e-01 1.12e+01 angle pdb=" CA TRP B 434 " pdb=" CB TRP B 434 " pdb=" CG TRP B 434 " ideal model delta sigma weight residual 113.60 119.93 -6.33 1.90e+00 2.77e-01 1.11e+01 angle pdb=" CA LYS A 771 " pdb=" CB LYS A 771 " pdb=" CG LYS A 771 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" C VAL A 326 " pdb=" N SER A 327 " pdb=" CA SER A 327 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" CA LYS B 771 " pdb=" CB LYS B 771 " pdb=" CG LYS B 771 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.38e+00 ... (remaining 12861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.52: 4820 18.52 - 37.03: 636 37.03 - 55.55: 114 55.55 - 74.07: 20 74.07 - 92.59: 10 Dihedral angle restraints: 5600 sinusoidal: 2216 harmonic: 3384 Sorted by residual: dihedral pdb=" CA TYR B 466 " pdb=" C TYR B 466 " pdb=" N ASN B 467 " pdb=" CA ASN B 467 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR A 466 " pdb=" C TYR A 466 " pdb=" N ASN A 467 " pdb=" CA ASN A 467 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASN B 328 " pdb=" C ASN B 328 " pdb=" N LEU B 329 " pdb=" CA LEU B 329 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1156 0.047 - 0.093: 270 0.093 - 0.140: 53 0.140 - 0.187: 8 0.187 - 0.233: 1 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CA CYS F 1 " pdb=" N CYS F 1 " pdb=" C CYS F 1 " pdb=" CB CYS F 1 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA GLU F 2 " pdb=" N GLU F 2 " pdb=" C GLU F 2 " pdb=" CB GLU F 2 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CG LEU B 248 " pdb=" CB LEU B 248 " pdb=" CD1 LEU B 248 " pdb=" CD2 LEU B 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1485 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 327 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER B 327 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 327 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN B 328 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 327 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C SER A 327 " 0.058 2.00e-02 2.50e+03 pdb=" O SER A 327 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 328 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 392 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO A 393 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " -0.032 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1550 2.76 - 3.47: 13696 3.47 - 4.19: 19913 4.19 - 4.90: 36858 Nonbonded interactions: 72019 Sorted by model distance: nonbonded pdb=" CD GLU F 2 " pdb=" N CYS H 1 " model vdw 1.330 3.350 nonbonded pdb=" CD GLU I 2 " pdb=" N CYS J 1 " model vdw 1.353 3.350 nonbonded pdb=" OE1 GLN A 499 " pdb=" ND2 ASN B 328 " model vdw 2.188 2.520 nonbonded pdb=" O GLU B 433 " pdb=" OG1 THR B 436 " model vdw 2.206 2.440 nonbonded pdb=" O SER A 322 " pdb=" OG SER A 322 " model vdw 2.219 2.440 ... (remaining 72014 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' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.990 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: 4.740 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.560 Find NCS groups from input model: 0.450 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 0.040 9496 Z= 0.235 Angle : 0.654 8.615 12866 Z= 0.347 Chirality : 0.041 0.233 1488 Planarity : 0.004 0.056 1626 Dihedral : 16.813 92.586 3432 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.70 % Allowed : 20.52 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1168 helix: 1.45 (0.19), residues: 762 sheet: -1.26 (0.55), residues: 54 loop : -2.35 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 434 HIS 0.005 0.001 HIS A 361 PHE 0.017 0.001 PHE A 332 TYR 0.015 0.001 TYR B 536 ARG 0.003 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.9146 (tt0) cc_final: 0.8856 (tt0) REVERT: A 338 GLN cc_start: 0.9059 (pt0) cc_final: 0.8811 (pp30) REVERT: A 346 GLU cc_start: 0.9085 (tt0) cc_final: 0.8864 (tt0) REVERT: A 415 LEU cc_start: 0.9393 (mt) cc_final: 0.9171 (tp) REVERT: A 566 ASP cc_start: 0.9385 (m-30) cc_final: 0.9171 (p0) REVERT: A 649 ILE cc_start: 0.8572 (mt) cc_final: 0.8325 (mm) REVERT: A 719 GLN cc_start: 0.8343 (mm110) cc_final: 0.8122 (tp40) REVERT: B 275 GLU cc_start: 0.9126 (tt0) cc_final: 0.8775 (tt0) REVERT: B 338 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8942 (pp30) REVERT: B 415 LEU cc_start: 0.9372 (mt) cc_final: 0.9154 (tp) REVERT: B 472 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 635 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8703 (mp) REVERT: B 649 ILE cc_start: 0.8656 (mt) cc_final: 0.8420 (mm) REVERT: B 719 GLN cc_start: 0.8300 (mm110) cc_final: 0.8054 (tp40) outliers start: 7 outliers final: 1 residues processed: 182 average time/residue: 0.2193 time to fit residues: 54.5664 Evaluate side-chains 104 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 635 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN A 825 GLN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B 825 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.006 0.056 9496 Z= 0.364 Angle : 0.655 10.723 12866 Z= 0.351 Chirality : 0.041 0.192 1488 Planarity : 0.005 0.061 1626 Dihedral : 6.004 76.691 1315 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.43 % Allowed : 22.64 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1168 helix: 1.77 (0.18), residues: 748 sheet: -0.81 (0.59), residues: 54 loop : -2.38 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 434 HIS 0.007 0.001 HIS B 361 PHE 0.022 0.002 PHE A 547 TYR 0.018 0.002 TYR A 465 ARG 0.006 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 99 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8550 (t80) REVERT: A 275 GLU cc_start: 0.9164 (tt0) cc_final: 0.8949 (tt0) REVERT: A 415 LEU cc_start: 0.9436 (mt) cc_final: 0.9182 (tp) REVERT: A 472 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 564 MET cc_start: 0.9365 (tmm) cc_final: 0.9106 (tmm) REVERT: A 635 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8787 (mp) REVERT: A 740 THR cc_start: 0.9115 (t) cc_final: 0.8875 (p) REVERT: B 355 GLU cc_start: 0.8766 (pt0) cc_final: 0.8409 (tm-30) REVERT: B 415 LEU cc_start: 0.9425 (mt) cc_final: 0.9170 (tp) REVERT: B 472 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8677 (mm-30) REVERT: B 629 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8473 (mtpt) REVERT: B 635 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8987 (mp) REVERT: B 733 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.9152 (mm-40) outliers start: 54 outliers final: 22 residues processed: 146 average time/residue: 0.1778 time to fit residues: 38.3230 Evaluate side-chains 118 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 733 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 84 optimal weight: 0.2980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9496 Z= 0.255 Angle : 0.563 8.238 12866 Z= 0.301 Chirality : 0.040 0.276 1488 Planarity : 0.004 0.052 1626 Dihedral : 5.649 74.577 1310 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.63 % Allowed : 25.65 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1168 helix: 1.97 (0.18), residues: 758 sheet: -0.64 (0.60), residues: 54 loop : -2.21 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 434 HIS 0.004 0.001 HIS B 361 PHE 0.026 0.002 PHE B 611 TYR 0.015 0.001 TYR A 465 ARG 0.005 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 83 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8458 (t80) REVERT: A 275 GLU cc_start: 0.9152 (tt0) cc_final: 0.8940 (tt0) REVERT: A 415 LEU cc_start: 0.9398 (mt) cc_final: 0.9171 (tp) REVERT: A 564 MET cc_start: 0.9369 (tmm) cc_final: 0.8976 (tmm) REVERT: A 635 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8871 (mp) REVERT: A 740 THR cc_start: 0.9322 (t) cc_final: 0.8822 (p) REVERT: A 798 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8797 (mmtm) REVERT: B 242 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8184 (t80) REVERT: B 275 GLU cc_start: 0.9170 (tt0) cc_final: 0.8943 (tt0) REVERT: B 355 GLU cc_start: 0.8799 (pt0) cc_final: 0.8403 (tm-30) REVERT: B 415 LEU cc_start: 0.9396 (mt) cc_final: 0.9162 (tp) REVERT: B 465 TYR cc_start: 0.5140 (m-80) cc_final: 0.4740 (m-80) REVERT: B 472 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8554 (mm-30) REVERT: B 629 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8454 (mtpt) REVERT: B 798 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8828 (mmtm) outliers start: 46 outliers final: 24 residues processed: 120 average time/residue: 0.1796 time to fit residues: 31.6090 Evaluate side-chains 112 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 671 GLN Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 0.0770 chunk 100 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 539 GLN B 501 GLN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9496 Z= 0.418 Angle : 0.639 9.819 12866 Z= 0.340 Chirality : 0.040 0.168 1488 Planarity : 0.004 0.055 1626 Dihedral : 5.511 67.794 1308 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.94 % Allowed : 26.06 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1168 helix: 1.86 (0.18), residues: 772 sheet: -0.62 (0.60), residues: 54 loop : -2.30 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 434 HIS 0.004 0.001 HIS A 361 PHE 0.019 0.002 PHE A 332 TYR 0.036 0.002 TYR B 818 ARG 0.003 0.000 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 80 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8322 (t80) REVERT: A 316 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8803 (tp-100) REVERT: A 415 LEU cc_start: 0.9469 (mt) cc_final: 0.9235 (tp) REVERT: A 564 MET cc_start: 0.9378 (tmm) cc_final: 0.9175 (tmm) REVERT: A 629 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8586 (mttt) REVERT: A 635 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8924 (mp) REVERT: A 740 THR cc_start: 0.9370 (t) cc_final: 0.9140 (t) REVERT: A 798 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8873 (mmtm) REVERT: B 242 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8146 (t80) REVERT: B 275 GLU cc_start: 0.9196 (tt0) cc_final: 0.8979 (tt0) REVERT: B 346 GLU cc_start: 0.9121 (tt0) cc_final: 0.8911 (tp30) REVERT: B 355 GLU cc_start: 0.8847 (pt0) cc_final: 0.8441 (tm-30) REVERT: B 415 LEU cc_start: 0.9453 (mt) cc_final: 0.9210 (tp) REVERT: B 472 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8683 (mm-30) REVERT: B 629 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8488 (mtpt) REVERT: B 635 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8949 (mp) REVERT: B 798 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8869 (mmtm) outliers start: 59 outliers final: 35 residues processed: 131 average time/residue: 0.1993 time to fit residues: 37.3104 Evaluate side-chains 120 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 76 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 821 MET Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 502 ASN A 719 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 502 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9496 Z= 0.226 Angle : 0.556 9.680 12866 Z= 0.293 Chirality : 0.038 0.164 1488 Planarity : 0.004 0.052 1626 Dihedral : 5.146 59.576 1308 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.23 % Allowed : 27.16 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.23 (0.25), residues: 1168 helix: 2.14 (0.18), residues: 772 sheet: -0.42 (0.61), residues: 54 loop : -2.24 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 434 HIS 0.003 0.001 HIS B 361 PHE 0.013 0.001 PHE A 332 TYR 0.036 0.001 TYR B 818 ARG 0.009 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 90 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8192 (t80) REVERT: A 316 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8786 (tp40) REVERT: A 415 LEU cc_start: 0.9421 (mt) cc_final: 0.9199 (tp) REVERT: A 564 MET cc_start: 0.9388 (tmm) cc_final: 0.9144 (tmm) REVERT: A 629 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8616 (mtpt) REVERT: A 635 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8941 (mp) REVERT: B 242 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8076 (t80) REVERT: B 275 GLU cc_start: 0.9140 (tt0) cc_final: 0.8929 (tt0) REVERT: B 415 LEU cc_start: 0.9405 (mt) cc_final: 0.9175 (tp) REVERT: B 472 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8674 (mm-30) REVERT: B 629 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8466 (mtpt) REVERT: B 635 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8957 (mp) REVERT: B 798 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8882 (mmtm) outliers start: 52 outliers final: 30 residues processed: 133 average time/residue: 0.1916 time to fit residues: 36.6977 Evaluate side-chains 118 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 80 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 502 ASN A 665 HIS B 501 GLN B 502 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9496 Z= 0.345 Angle : 0.632 9.754 12866 Z= 0.333 Chirality : 0.040 0.312 1488 Planarity : 0.004 0.051 1626 Dihedral : 5.096 51.830 1308 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.04 % Allowed : 27.06 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.06 (0.24), residues: 1168 helix: 2.05 (0.18), residues: 764 sheet: -0.53 (0.60), residues: 54 loop : -2.30 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 434 HIS 0.004 0.001 HIS B 361 PHE 0.018 0.002 PHE A 332 TYR 0.041 0.002 TYR A 818 ARG 0.007 0.000 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 81 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8050 (t80) REVERT: A 316 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8804 (tp40) REVERT: A 415 LEU cc_start: 0.9486 (mt) cc_final: 0.9263 (tp) REVERT: A 564 MET cc_start: 0.9400 (tmm) cc_final: 0.9160 (tmm) REVERT: A 629 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8612 (mtpt) REVERT: A 750 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 818 TYR cc_start: 0.8600 (m-10) cc_final: 0.8356 (m-10) REVERT: B 242 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 275 GLU cc_start: 0.9172 (tt0) cc_final: 0.8947 (tt0) REVERT: B 415 LEU cc_start: 0.9477 (mt) cc_final: 0.9256 (tp) REVERT: B 629 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8583 (mtpt) REVERT: B 798 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8923 (mmtm) outliers start: 60 outliers final: 34 residues processed: 132 average time/residue: 0.1862 time to fit residues: 35.8827 Evaluate side-chains 122 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 81 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 501 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9496 Z= 0.178 Angle : 0.566 11.775 12866 Z= 0.291 Chirality : 0.038 0.257 1488 Planarity : 0.003 0.051 1626 Dihedral : 4.723 57.042 1308 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.02 % Allowed : 29.18 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.42 (0.25), residues: 1168 helix: 2.32 (0.18), residues: 762 sheet: -0.37 (0.62), residues: 54 loop : -2.11 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 434 HIS 0.002 0.001 HIS B 361 PHE 0.010 0.001 PHE A 332 TYR 0.018 0.001 TYR A 818 ARG 0.004 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7857 (t80) REVERT: A 415 LEU cc_start: 0.9363 (mt) cc_final: 0.9145 (tp) REVERT: A 564 MET cc_start: 0.9393 (tmm) cc_final: 0.9145 (tmm) REVERT: A 629 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8581 (mttt) REVERT: A 799 ASP cc_start: 0.7975 (t70) cc_final: 0.7687 (t70) REVERT: B 275 GLU cc_start: 0.9138 (tt0) cc_final: 0.8919 (tt0) REVERT: B 415 LEU cc_start: 0.9346 (mt) cc_final: 0.9136 (tp) REVERT: B 629 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8533 (mtpt) REVERT: B 733 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.9211 (mm-40) REVERT: B 798 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8929 (mmtm) outliers start: 40 outliers final: 22 residues processed: 128 average time/residue: 0.1928 time to fit residues: 35.3339 Evaluate side-chains 110 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 501 GLN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9496 Z= 0.176 Angle : 0.545 10.809 12866 Z= 0.283 Chirality : 0.037 0.234 1488 Planarity : 0.004 0.073 1626 Dihedral : 4.549 56.887 1308 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.02 % Allowed : 29.58 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1168 helix: 2.42 (0.18), residues: 762 sheet: -0.21 (0.65), residues: 54 loop : -2.10 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 434 HIS 0.004 0.001 HIS A 361 PHE 0.009 0.001 PHE B 332 TYR 0.034 0.001 TYR A 818 ARG 0.008 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7791 (t80) REVERT: A 316 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8786 (tp40) REVERT: A 415 LEU cc_start: 0.9329 (mt) cc_final: 0.9117 (tp) REVERT: A 564 MET cc_start: 0.9409 (tmm) cc_final: 0.9161 (tmm) REVERT: A 629 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8599 (mtpt) REVERT: A 750 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8670 (tt) REVERT: B 275 GLU cc_start: 0.9131 (tt0) cc_final: 0.8918 (tt0) REVERT: B 415 LEU cc_start: 0.9324 (mt) cc_final: 0.9112 (tp) REVERT: B 773 CYS cc_start: 0.8883 (p) cc_final: 0.8640 (p) REVERT: B 798 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8942 (mmtm) REVERT: B 799 ASP cc_start: 0.7910 (t70) cc_final: 0.7594 (t70) outliers start: 30 outliers final: 18 residues processed: 112 average time/residue: 0.1888 time to fit residues: 30.7146 Evaluate side-chains 103 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9496 Z= 0.183 Angle : 0.564 11.689 12866 Z= 0.289 Chirality : 0.038 0.208 1488 Planarity : 0.003 0.053 1626 Dihedral : 4.462 56.999 1308 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.62 % Allowed : 28.67 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.65 (0.25), residues: 1168 helix: 2.49 (0.18), residues: 760 sheet: -0.13 (0.65), residues: 54 loop : -1.99 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 434 HIS 0.003 0.001 HIS A 361 PHE 0.009 0.001 PHE A 332 TYR 0.018 0.001 TYR B 818 ARG 0.007 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7827 (t80) REVERT: A 316 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8778 (tp40) REVERT: A 415 LEU cc_start: 0.9309 (mt) cc_final: 0.9104 (tp) REVERT: A 564 MET cc_start: 0.9398 (tmm) cc_final: 0.9145 (tmm) REVERT: A 629 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8601 (mtpt) REVERT: A 750 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 799 ASP cc_start: 0.7988 (t70) cc_final: 0.7687 (t70) REVERT: B 275 GLU cc_start: 0.9132 (tt0) cc_final: 0.8921 (tt0) REVERT: B 415 LEU cc_start: 0.9282 (mt) cc_final: 0.9077 (tp) REVERT: B 629 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8451 (mttt) REVERT: B 733 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.9249 (mm-40) REVERT: B 773 CYS cc_start: 0.8892 (p) cc_final: 0.8640 (p) REVERT: B 798 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8959 (mmtm) REVERT: B 799 ASP cc_start: 0.7871 (t70) cc_final: 0.7429 (t70) outliers start: 36 outliers final: 24 residues processed: 120 average time/residue: 0.1774 time to fit residues: 31.4884 Evaluate side-chains 113 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 82 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN B 502 ASN B 665 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9496 Z= 0.292 Angle : 0.630 11.806 12866 Z= 0.325 Chirality : 0.039 0.200 1488 Planarity : 0.004 0.050 1626 Dihedral : 4.572 56.586 1308 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.82 % Allowed : 29.78 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 (0.25), residues: 1168 helix: 2.35 (0.18), residues: 762 sheet: -0.29 (0.64), residues: 54 loop : -2.04 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 334 HIS 0.004 0.001 HIS A 361 PHE 0.017 0.001 PHE A 332 TYR 0.034 0.002 TYR B 818 ARG 0.008 0.000 ARG B 435 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.7955 (t80) REVERT: A 316 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8767 (tp40) REVERT: A 415 LEU cc_start: 0.9410 (mt) cc_final: 0.9193 (tp) REVERT: A 564 MET cc_start: 0.9408 (tmm) cc_final: 0.9142 (tmm) REVERT: A 629 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8570 (mtpt) REVERT: A 750 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 773 CYS cc_start: 0.8963 (p) cc_final: 0.8735 (p) REVERT: A 799 ASP cc_start: 0.7990 (t70) cc_final: 0.7529 (t70) REVERT: A 818 TYR cc_start: 0.8346 (m-10) cc_final: 0.8029 (m-80) REVERT: B 275 GLU cc_start: 0.9169 (tt0) cc_final: 0.8941 (tt0) REVERT: B 415 LEU cc_start: 0.9405 (mt) cc_final: 0.9193 (tp) REVERT: B 629 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8560 (mttt) REVERT: B 773 CYS cc_start: 0.8869 (p) cc_final: 0.8626 (p) REVERT: B 798 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8955 (mmtm) REVERT: B 799 ASP cc_start: 0.7792 (t70) cc_final: 0.7479 (t70) REVERT: B 818 TYR cc_start: 0.8680 (m-10) cc_final: 0.8347 (m-80) outliers start: 28 outliers final: 21 residues processed: 107 average time/residue: 0.1874 time to fit residues: 29.6650 Evaluate side-chains 107 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 798 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 94 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN B 502 ASN B 719 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.079957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054575 restraints weight = 30144.492| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.78 r_work: 0.2904 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9496 Z= 0.254 Angle : 0.610 11.343 12866 Z= 0.313 Chirality : 0.039 0.214 1488 Planarity : 0.004 0.049 1626 Dihedral : 4.574 59.576 1308 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.32 % Allowed : 29.28 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.45 (0.24), residues: 1168 helix: 2.34 (0.18), residues: 762 sheet: -0.38 (0.64), residues: 54 loop : -2.08 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 334 HIS 0.004 0.001 HIS B 361 PHE 0.013 0.001 PHE A 332 TYR 0.040 0.002 TYR B 818 ARG 0.008 0.000 ARG B 435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.13 seconds wall clock time: 36 minutes 21.50 seconds (2181.50 seconds total)