Starting phenix.real_space_refine on Sun Apr 7 01:12:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dz7_8931/04_2024/6dz7_8931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dz7_8931/04_2024/6dz7_8931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dz7_8931/04_2024/6dz7_8931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dz7_8931/04_2024/6dz7_8931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dz7_8931/04_2024/6dz7_8931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dz7_8931/04_2024/6dz7_8931.pdb" } resolution = 3.89 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6098 2.51 5 N 1534 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 710": "NH1" <-> "NH2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 710": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9284 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4642 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 26, 'TRANS': 547} Chain breaks: 9 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4642 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 26, 'TRANS': 547} Chain breaks: 9 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 5.46, per 1000 atoms: 0.59 Number of scatterers: 9284 At special positions: 0 Unit cell: (129.34, 75.6309, 100.841, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1614 8.00 N 1534 7.00 C 6098 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=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 2 sheets defined 69.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 68 through 86 removed outlier: 3.625A pdb=" N TYR B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.671A pdb=" N THR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 200 removed outlier: 4.539A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.619A pdb=" N THR B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 312 removed outlier: 3.549A pdb=" N TYR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Proline residue: B 285 - end of helix Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 322 through 349 removed outlier: 3.815A pdb=" N ILE B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.919A pdb=" N ALA B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 386 removed outlier: 3.781A pdb=" N LYS B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 425 through 448 removed outlier: 4.054A pdb=" N ILE B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 502 removed outlier: 3.516A pdb=" N GLU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 525 removed outlier: 3.533A pdb=" N LEU B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 553 removed outlier: 5.616A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.852A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 635 removed outlier: 3.874A pdb=" N LEU B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 658 removed outlier: 4.412A pdb=" N GLU B 646 " --> pdb=" O ARG B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 68 through 86 removed outlier: 3.626A pdb=" N TYR A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.670A pdb=" N THR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 200 removed outlier: 4.540A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.619A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 312 removed outlier: 3.549A pdb=" N TYR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 322 through 349 removed outlier: 3.815A pdb=" N ILE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.919A pdb=" N ALA A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 386 removed outlier: 3.781A pdb=" N LYS A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 425 through 448 removed outlier: 4.054A pdb=" N ILE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLN A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 502 removed outlier: 3.516A pdb=" N GLU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 removed outlier: 3.532A pdb=" N LEU A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 553 removed outlier: 5.616A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.852A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 635 removed outlier: 3.874A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 658 removed outlier: 4.411A pdb=" N GLU A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 21 removed outlier: 7.768A pdb=" N TYR B 18 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG B 65 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 20 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE B 63 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N VAL B 62 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL B 52 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 64 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR B 50 " --> pdb=" O VAL B 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 7.768A pdb=" N TYR A 18 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG A 65 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 20 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE A 63 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL A 62 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N VAL A 52 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 64 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR A 50 " --> pdb=" O VAL A 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 570 hydrogen bonds defined for protein. 1710 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: 2.51 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2703 1.34 - 1.46: 1989 1.46 - 1.57: 4770 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 9518 Sorted by residual: bond pdb=" C VAL B 448 " pdb=" N PRO B 449 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.72e+00 bond pdb=" C VAL A 448 " pdb=" N PRO A 449 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.69e+00 bond pdb=" CB ASN A 370 " pdb=" CG ASN A 370 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.45e+00 bond pdb=" CB ASN B 370 " pdb=" CG ASN B 370 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.41e+00 bond pdb=" CG1 ILE A 221 " pdb=" CD1 ILE A 221 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.30e+00 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.20: 180 105.20 - 112.48: 4759 112.48 - 119.75: 3475 119.75 - 127.03: 4373 127.03 - 134.31: 149 Bond angle restraints: 12936 Sorted by residual: angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 108.88 120.83 -11.95 2.16e+00 2.14e-01 3.06e+01 angle pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 108.88 120.81 -11.93 2.16e+00 2.14e-01 3.05e+01 angle pdb=" C GLU B 132 " pdb=" N TRP B 133 " pdb=" CA TRP B 133 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.93e+01 angle pdb=" C GLU A 132 " pdb=" N TRP A 133 " pdb=" CA TRP A 133 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.93e+01 angle pdb=" N GLU B 94 " pdb=" CA GLU B 94 " pdb=" C GLU B 94 " ideal model delta sigma weight residual 109.81 119.61 -9.80 2.21e+00 2.05e-01 1.97e+01 ... (remaining 12931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 5192 15.89 - 31.77: 300 31.77 - 47.66: 94 47.66 - 63.54: 2 63.54 - 79.43: 8 Dihedral angle restraints: 5596 sinusoidal: 2200 harmonic: 3396 Sorted by residual: dihedral pdb=" CA TRP A 155 " pdb=" C TRP A 155 " pdb=" N SER A 156 " pdb=" CA SER A 156 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA TRP B 155 " pdb=" C TRP B 155 " pdb=" N SER B 156 " pdb=" CA SER B 156 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ILE A 27 " pdb=" C ILE A 27 " pdb=" N ASP A 28 " pdb=" CA ASP A 28 " ideal model delta harmonic sigma weight residual 180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 5593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1019 0.060 - 0.121: 347 0.121 - 0.181: 86 0.181 - 0.241: 18 0.241 - 0.302: 4 Chirality restraints: 1474 Sorted by residual: chirality pdb=" CB VAL B 117 " pdb=" CA VAL B 117 " pdb=" CG1 VAL B 117 " pdb=" CG2 VAL B 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB VAL A 117 " pdb=" CA VAL A 117 " pdb=" CG1 VAL A 117 " pdb=" CG2 VAL A 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE B 323 " pdb=" CA ILE B 323 " pdb=" CG1 ILE B 323 " pdb=" CG2 ILE B 323 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1471 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 637 " 0.063 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO B 638 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 638 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 638 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 637 " -0.063 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO A 638 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 372 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ILE B 372 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE B 372 " 0.021 2.00e-02 2.50e+03 pdb=" N THR B 373 " 0.019 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2850 2.82 - 3.34: 9208 3.34 - 3.86: 15105 3.86 - 4.38: 15828 4.38 - 4.90: 26691 Nonbonded interactions: 69682 Sorted by model distance: nonbonded pdb=" O TYR B 432 " pdb=" OG1 THR B 436 " model vdw 2.305 2.440 nonbonded pdb=" O TYR A 432 " pdb=" OG1 THR A 436 " model vdw 2.305 2.440 nonbonded pdb=" OD1 ASP B 510 " pdb=" NH2 ARG B 513 " model vdw 2.316 2.520 nonbonded pdb=" OD1 ASP A 510 " pdb=" NH2 ARG A 513 " model vdw 2.316 2.520 nonbonded pdb=" O MET A 152 " pdb=" NH2 ARG A 545 " model vdw 2.357 2.520 ... (remaining 69677 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.010 0.087 9518 Z= 0.609 Angle : 1.252 11.953 12936 Z= 0.671 Chirality : 0.066 0.302 1474 Planarity : 0.009 0.097 1600 Dihedral : 11.475 79.430 3376 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 0.20 % Allowed : 4.67 % Favored : 95.13 % 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: -3.82 (0.21), residues: 1108 helix: -1.69 (0.15), residues: 784 sheet: -5.00 (0.81), residues: 20 loop : -4.31 (0.28), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP B 227 HIS 0.017 0.005 HIS B 130 PHE 0.021 0.003 PHE B 140 TYR 0.026 0.003 TYR B 187 ARG 0.012 0.002 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7804 (p90) cc_final: 0.7565 (p90) REVERT: B 335 MET cc_start: 0.8369 (mmm) cc_final: 0.8119 (mmt) REVERT: A 192 MET cc_start: 0.8079 (ptt) cc_final: 0.7835 (ptm) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.2945 time to fit residues: 45.6279 Evaluate side-chains 44 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 176 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN A 176 HIS A 280 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9518 Z= 0.233 Angle : 0.735 8.929 12936 Z= 0.381 Chirality : 0.043 0.250 1474 Planarity : 0.006 0.078 1600 Dihedral : 5.607 25.318 1248 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 2.33 % Allowed : 8.72 % Favored : 88.95 % 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: -1.70 (0.25), residues: 1108 helix: 0.00 (0.18), residues: 794 sheet: -4.75 (0.80), residues: 20 loop : -3.97 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 706 HIS 0.004 0.001 HIS B 619 PHE 0.019 0.001 PHE A 616 TYR 0.011 0.001 TYR A 180 ARG 0.006 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: B 190 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: B 286 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7999 (t80) REVERT: B 335 MET cc_start: 0.8253 (mmm) cc_final: 0.7995 (mmt) REVERT: A 294 LEU cc_start: 0.9433 (tp) cc_final: 0.9227 (tt) REVERT: A 340 LEU cc_start: 0.9110 (tt) cc_final: 0.8832 (mt) REVERT: A 641 ARG cc_start: 0.8504 (ttt90) cc_final: 0.7941 (ptt90) REVERT: A 707 MET cc_start: 0.8130 (mpp) cc_final: 0.7904 (mpp) outliers start: 23 outliers final: 6 residues processed: 90 average time/residue: 0.2190 time to fit residues: 27.9774 Evaluate side-chains 57 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 588 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 0.0020 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9518 Z= 0.169 Angle : 0.659 7.638 12936 Z= 0.334 Chirality : 0.041 0.184 1474 Planarity : 0.005 0.065 1600 Dihedral : 4.924 21.669 1248 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.14 % Allowed : 9.13 % Favored : 87.73 % 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: -0.84 (0.26), residues: 1108 helix: 0.68 (0.19), residues: 794 sheet: -4.37 (0.78), residues: 20 loop : -3.79 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 706 HIS 0.003 0.001 HIS B 176 PHE 0.013 0.001 PHE A 616 TYR 0.008 0.001 TYR A 589 ARG 0.009 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: B 190 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: B 192 MET cc_start: 0.8260 (ttp) cc_final: 0.7956 (ttp) REVERT: A 340 LEU cc_start: 0.9090 (tt) cc_final: 0.8848 (mt) REVERT: A 545 ARG cc_start: 0.7944 (mmp-170) cc_final: 0.6596 (ptp-170) outliers start: 31 outliers final: 13 residues processed: 96 average time/residue: 0.2126 time to fit residues: 29.1536 Evaluate side-chains 68 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9518 Z= 0.214 Angle : 0.673 13.459 12936 Z= 0.337 Chirality : 0.041 0.190 1474 Planarity : 0.005 0.065 1600 Dihedral : 4.766 22.323 1248 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 2.03 % Allowed : 12.27 % Favored : 85.70 % 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: -0.38 (0.26), residues: 1108 helix: 1.02 (0.19), residues: 798 sheet: -4.16 (0.81), residues: 20 loop : -3.70 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 155 HIS 0.004 0.001 HIS A 130 PHE 0.016 0.001 PHE B 433 TYR 0.009 0.001 TYR B 180 ARG 0.008 0.001 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8324 (ttp) cc_final: 0.8003 (ttp) REVERT: A 340 LEU cc_start: 0.9084 (tt) cc_final: 0.8883 (mt) REVERT: A 514 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8066 (mp0) REVERT: A 545 ARG cc_start: 0.7957 (mmp-170) cc_final: 0.6535 (ptp-170) REVERT: A 611 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8481 (mp) outliers start: 20 outliers final: 14 residues processed: 75 average time/residue: 0.2069 time to fit residues: 22.9769 Evaluate side-chains 65 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 50 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9518 Z= 0.195 Angle : 0.661 15.100 12936 Z= 0.326 Chirality : 0.041 0.200 1474 Planarity : 0.005 0.062 1600 Dihedral : 4.631 21.481 1248 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.13 % Allowed : 12.58 % Favored : 85.29 % 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: -0.03 (0.27), residues: 1108 helix: 1.28 (0.19), residues: 792 sheet: -3.93 (0.85), residues: 20 loop : -3.46 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 541 HIS 0.003 0.001 HIS A 619 PHE 0.012 0.001 PHE B 549 TYR 0.008 0.001 TYR B 180 ARG 0.006 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8369 (ttp) cc_final: 0.8057 (ttp) REVERT: B 294 LEU cc_start: 0.9335 (tp) cc_final: 0.9080 (tt) REVERT: A 340 LEU cc_start: 0.9103 (tt) cc_final: 0.8900 (mt) outliers start: 21 outliers final: 19 residues processed: 70 average time/residue: 0.2000 time to fit residues: 20.5760 Evaluate side-chains 66 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 91 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 ASN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9518 Z= 0.346 Angle : 0.740 9.790 12936 Z= 0.379 Chirality : 0.044 0.190 1474 Planarity : 0.005 0.065 1600 Dihedral : 4.978 23.605 1248 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 3.96 % Allowed : 11.26 % Favored : 84.79 % 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: -0.01 (0.27), residues: 1108 helix: 1.21 (0.19), residues: 800 sheet: -3.73 (1.00), residues: 20 loop : -3.34 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 541 HIS 0.006 0.002 HIS A 130 PHE 0.013 0.002 PHE A 173 TYR 0.021 0.002 TYR A 506 ARG 0.007 0.001 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 48 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: B 152 MET cc_start: 0.8475 (tpt) cc_final: 0.7888 (tpt) REVERT: B 192 MET cc_start: 0.8467 (ttp) cc_final: 0.8162 (ttp) REVERT: B 524 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8942 (mp) REVERT: A 611 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 641 ARG cc_start: 0.7233 (ptt-90) cc_final: 0.6870 (ptp90) outliers start: 39 outliers final: 25 residues processed: 84 average time/residue: 0.2311 time to fit residues: 28.7160 Evaluate side-chains 72 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 45 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 707 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9518 Z= 0.194 Angle : 0.662 10.134 12936 Z= 0.330 Chirality : 0.041 0.189 1474 Planarity : 0.005 0.060 1600 Dihedral : 4.692 21.432 1248 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.54 % Allowed : 13.49 % Favored : 83.98 % 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: 0.29 (0.27), residues: 1108 helix: 1.49 (0.19), residues: 792 sheet: -3.68 (0.96), residues: 20 loop : -3.27 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 541 HIS 0.003 0.001 HIS B 619 PHE 0.013 0.001 PHE A 253 TYR 0.008 0.001 TYR B 506 ARG 0.008 0.000 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: B 152 MET cc_start: 0.8353 (tpt) cc_final: 0.7759 (tpt) REVERT: B 192 MET cc_start: 0.8480 (ttp) cc_final: 0.8175 (ttp) REVERT: B 524 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8765 (mp) REVERT: B 545 ARG cc_start: 0.8074 (mmm160) cc_final: 0.6673 (ptp-170) REVERT: A 39 LEU cc_start: 0.7963 (pp) cc_final: 0.7753 (pp) REVERT: A 340 LEU cc_start: 0.9152 (tt) cc_final: 0.8891 (mt) REVERT: A 515 MET cc_start: 0.8538 (tmm) cc_final: 0.8279 (tmm) REVERT: A 641 ARG cc_start: 0.7009 (ptt-90) cc_final: 0.6680 (ptt-90) outliers start: 25 outliers final: 19 residues processed: 72 average time/residue: 0.2085 time to fit residues: 21.8316 Evaluate side-chains 64 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 707 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9518 Z= 0.202 Angle : 0.664 10.775 12936 Z= 0.329 Chirality : 0.040 0.187 1474 Planarity : 0.005 0.059 1600 Dihedral : 4.567 22.178 1248 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 2.54 % Allowed : 13.49 % Favored : 83.98 % 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: 0.49 (0.27), residues: 1108 helix: 1.60 (0.19), residues: 786 sheet: -3.41 (1.03), residues: 20 loop : -2.99 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 541 HIS 0.003 0.001 HIS A 130 PHE 0.011 0.001 PHE A 549 TYR 0.009 0.001 TYR B 506 ARG 0.005 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 47 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: B 152 MET cc_start: 0.8393 (tpt) cc_final: 0.7797 (tpt) REVERT: B 192 MET cc_start: 0.8435 (ttp) cc_final: 0.8122 (ttp) REVERT: B 524 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8807 (mp) REVERT: B 545 ARG cc_start: 0.7763 (mmm160) cc_final: 0.6635 (ptp-170) REVERT: A 39 LEU cc_start: 0.7966 (pp) cc_final: 0.7747 (pp) REVERT: A 340 LEU cc_start: 0.9211 (tt) cc_final: 0.8851 (mp) REVERT: A 515 MET cc_start: 0.8577 (tmm) cc_final: 0.8356 (tmm) REVERT: A 641 ARG cc_start: 0.6828 (ptt-90) cc_final: 0.6485 (ptt-90) outliers start: 25 outliers final: 21 residues processed: 69 average time/residue: 0.2152 time to fit residues: 22.0385 Evaluate side-chains 67 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 707 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9518 Z= 0.183 Angle : 0.640 10.053 12936 Z= 0.318 Chirality : 0.040 0.183 1474 Planarity : 0.005 0.059 1600 Dihedral : 4.439 20.612 1248 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.43 % Allowed : 13.89 % Favored : 83.67 % 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: 0.59 (0.27), residues: 1108 helix: 1.67 (0.19), residues: 786 sheet: -3.29 (1.04), residues: 20 loop : -2.97 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 541 HIS 0.003 0.001 HIS A 130 PHE 0.011 0.001 PHE B 549 TYR 0.009 0.001 TYR B 180 ARG 0.005 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: B 152 MET cc_start: 0.8376 (tpt) cc_final: 0.7997 (tpt) REVERT: B 192 MET cc_start: 0.8445 (ttp) cc_final: 0.8138 (ttp) REVERT: B 282 LEU cc_start: 0.7699 (tp) cc_final: 0.6760 (mm) REVERT: B 524 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8741 (mp) REVERT: B 545 ARG cc_start: 0.7605 (mmm160) cc_final: 0.6444 (ptp-170) REVERT: A 39 LEU cc_start: 0.7927 (pp) cc_final: 0.7705 (pp) REVERT: A 340 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8861 (mp) REVERT: A 515 MET cc_start: 0.8584 (tmm) cc_final: 0.8375 (tmm) outliers start: 24 outliers final: 20 residues processed: 68 average time/residue: 0.1900 time to fit residues: 19.9831 Evaluate side-chains 70 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 707 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9518 Z= 0.177 Angle : 0.641 9.813 12936 Z= 0.317 Chirality : 0.040 0.188 1474 Planarity : 0.005 0.058 1600 Dihedral : 4.361 20.346 1248 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.23 % Allowed : 14.20 % Favored : 83.57 % 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: 0.65 (0.27), residues: 1108 helix: 1.74 (0.19), residues: 784 sheet: -3.16 (1.05), residues: 20 loop : -2.98 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 227 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE B 549 TYR 0.009 0.001 TYR B 180 ARG 0.004 0.000 ARG A 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: B 152 MET cc_start: 0.8391 (tpt) cc_final: 0.7986 (tpt) REVERT: B 192 MET cc_start: 0.8493 (ttp) cc_final: 0.8191 (ttp) REVERT: B 282 LEU cc_start: 0.7680 (tp) cc_final: 0.6537 (mt) REVERT: B 524 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8777 (mp) REVERT: B 545 ARG cc_start: 0.7581 (mmm160) cc_final: 0.6592 (ptp-170) REVERT: A 39 LEU cc_start: 0.7910 (pp) cc_final: 0.7691 (pp) REVERT: A 340 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8864 (mp) outliers start: 22 outliers final: 19 residues processed: 69 average time/residue: 0.2188 time to fit residues: 23.7694 Evaluate side-chains 67 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 707 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060980 restraints weight = 42513.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062328 restraints weight = 26055.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063271 restraints weight = 18705.054| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9518 Z= 0.163 Angle : 0.636 10.588 12936 Z= 0.311 Chirality : 0.039 0.180 1474 Planarity : 0.004 0.058 1600 Dihedral : 4.232 19.709 1248 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.23 % Allowed : 14.71 % Favored : 83.06 % 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: 0.64 (0.27), residues: 1108 helix: 1.79 (0.19), residues: 782 sheet: -2.90 (1.07), residues: 20 loop : -3.16 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 227 HIS 0.003 0.001 HIS B 619 PHE 0.012 0.001 PHE A 61 TYR 0.008 0.001 TYR B 180 ARG 0.004 0.000 ARG A 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.70 seconds wall clock time: 30 minutes 34.80 seconds (1834.80 seconds total)