Starting phenix.real_space_refine on Thu Feb 15 01:03:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qma_4593/02_2024/6qma_4593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qma_4593/02_2024/6qma_4593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qma_4593/02_2024/6qma_4593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qma_4593/02_2024/6qma_4593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qma_4593/02_2024/6qma_4593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qma_4593/02_2024/6qma_4593.pdb" } resolution = 3.7 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= 0.011 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 Ca 4 9.91 5 S 40 5.16 5 C 6970 2.51 5 N 1786 2.21 5 O 1916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B ASP 556": "OD1" <-> "OD2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10716 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5356 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 28, 'TRANS': 633} Chain breaks: 5 Chain: "B" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5356 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 28, 'TRANS': 633} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.01, per 1000 atoms: 0.56 Number of scatterers: 10716 At special positions: 0 Unit cell: (120.428, 110.308, 106.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 40 16.00 O 1916 8.00 N 1786 7.00 C 6970 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 74.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.720A pdb=" N HIS A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 152 through 166 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.827A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 211 removed outlier: 4.864A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.659A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 318 removed outlier: 4.135A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 325 through 358 Proline residue: A 332 - end of helix Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 362 through 391 removed outlier: 6.152A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.673A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.624A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.507A pdb=" N GLU A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 482 through 495 removed outlier: 3.543A pdb=" N ARG A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.876A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.225A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 585 removed outlier: 4.152A pdb=" N THR A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 Processing helix chain 'A' and resid 629 through 650 removed outlier: 3.937A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 3.509A pdb=" N ILE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 696 Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'B' and resid 32 through 50 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.720A pdb=" N HIS B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.827A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 211 removed outlier: 4.864A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.659A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 318 removed outlier: 4.134A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Proline residue: B 293 - end of helix Processing helix chain 'B' and resid 325 through 358 Proline residue: B 332 - end of helix Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 362 through 391 removed outlier: 6.152A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 415 removed outlier: 3.673A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.623A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 468 Processing helix chain 'B' and resid 477 through 481 removed outlier: 3.508A pdb=" N GLU B 480 " --> pdb=" O GLU B 477 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 481 " --> pdb=" O ASP B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 477 through 481' Processing helix chain 'B' and resid 482 through 495 removed outlier: 3.543A pdb=" N ARG B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.877A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 543 removed outlier: 4.226A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 585 removed outlier: 4.152A pdb=" N THR B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 Processing helix chain 'B' and resid 629 through 650 removed outlier: 3.937A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 684 removed outlier: 3.510A pdb=" N ILE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 700 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.102A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.708A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.102A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.707A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 4.48 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: 3337 1.34 - 1.46: 1926 1.46 - 1.57: 5663 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 10992 Sorted by residual: bond pdb=" C ILE B 292 " pdb=" N PRO B 293 " ideal model delta sigma weight residual 1.335 1.393 -0.059 1.28e-02 6.10e+03 2.10e+01 bond pdb=" C ILE A 292 " pdb=" N PRO A 293 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.28e-02 6.10e+03 2.08e+01 bond pdb=" C THR A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 1.335 1.391 -0.055 1.36e-02 5.41e+03 1.67e+01 bond pdb=" C THR B 340 " pdb=" N PRO B 341 " ideal model delta sigma weight residual 1.335 1.391 -0.055 1.36e-02 5.41e+03 1.65e+01 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.94e+00 ... (remaining 10987 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.18: 251 106.18 - 113.17: 5834 113.17 - 120.17: 4090 120.17 - 127.16: 4582 127.16 - 134.16: 153 Bond angle restraints: 14910 Sorted by residual: angle pdb=" C VAL A 454 " pdb=" N VAL A 455 " pdb=" CA VAL A 455 " ideal model delta sigma weight residual 120.33 124.43 -4.10 8.00e-01 1.56e+00 2.63e+01 angle pdb=" C VAL B 454 " pdb=" N VAL B 455 " pdb=" CA VAL B 455 " ideal model delta sigma weight residual 120.33 124.40 -4.07 8.00e-01 1.56e+00 2.59e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" CB VAL A 248 " ideal model delta sigma weight residual 112.28 106.95 5.33 1.33e+00 5.65e-01 1.61e+01 angle pdb=" N VAL B 248 " pdb=" CA VAL B 248 " pdb=" CB VAL B 248 " ideal model delta sigma weight residual 112.28 106.95 5.33 1.33e+00 5.65e-01 1.60e+01 angle pdb=" N ILE A 543 " pdb=" CA ILE A 543 " pdb=" C ILE A 543 " ideal model delta sigma weight residual 112.50 107.23 5.27 1.39e+00 5.18e-01 1.44e+01 ... (remaining 14905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5694 17.22 - 34.44: 598 34.44 - 51.67: 128 51.67 - 68.89: 20 68.89 - 86.11: 20 Dihedral angle restraints: 6460 sinusoidal: 2592 harmonic: 3868 Sorted by residual: dihedral pdb=" CA GLN A 648 " pdb=" C GLN A 648 " pdb=" N GLU A 649 " pdb=" CA GLU A 649 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLN B 648 " pdb=" C GLN B 648 " pdb=" N GLU B 649 " pdb=" CA GLU B 649 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA THR B 135 " pdb=" C THR B 135 " pdb=" N PRO B 136 " pdb=" CA PRO B 136 " ideal model delta harmonic sigma weight residual 180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1253 0.051 - 0.101: 258 0.101 - 0.151: 109 0.151 - 0.202: 8 0.202 - 0.252: 4 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL B 248 " pdb=" CA VAL B 248 " pdb=" CG1 VAL B 248 " pdb=" CG2 VAL B 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL B 500 " pdb=" CA VAL B 500 " pdb=" CG1 VAL B 500 " pdb=" CG2 VAL B 500 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1629 not shown) Planarity restraints: 1894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 532 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C ASN B 532 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN B 532 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP B 533 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 532 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C ASN A 532 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN A 532 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP A 533 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 402 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.038 5.00e-02 4.00e+02 ... (remaining 1891 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 80 2.56 - 3.14: 8263 3.14 - 3.73: 17645 3.73 - 4.31: 22665 4.31 - 4.90: 37794 Nonbonded interactions: 86447 Sorted by model distance: nonbonded pdb=" OE2 GLU A 313 " pdb=" OD1 ASN A 317 " model vdw 1.974 3.040 nonbonded pdb=" OE2 GLU B 313 " pdb=" OD1 ASN B 317 " model vdw 1.974 3.040 nonbonded pdb=" OE1 GLN B 445 " pdb=" ND2 ASN B 531 " model vdw 2.294 2.520 nonbonded pdb=" OE1 GLN A 445 " pdb=" ND2 ASN A 531 " model vdw 2.294 2.520 nonbonded pdb=" O TYR B 120 " pdb=" OG1 THR B 124 " model vdw 2.307 2.440 ... (remaining 86442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 3.590 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.290 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.006 0.065 10992 Z= 0.356 Angle : 0.880 11.150 14910 Z= 0.508 Chirality : 0.050 0.252 1632 Planarity : 0.007 0.067 1894 Dihedral : 15.235 86.108 3948 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.18 % Allowed : 7.56 % Favored : 92.27 % 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: -3.00 (0.18), residues: 1300 helix: -1.54 (0.13), residues: 934 sheet: -2.21 (0.62), residues: 68 loop : -2.77 (0.29), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 235 HIS 0.006 0.001 HIS B 143 PHE 0.032 0.002 PHE A 396 TYR 0.021 0.002 TYR B 279 ARG 0.004 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7960 (tpp80) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.2608 time to fit residues: 59.3407 Evaluate side-chains 119 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.0020 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 317 ASN A 378 ASN A 435 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 317 ASN B 378 ASN B 435 ASN B 641 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10992 Z= 0.190 Angle : 0.554 8.073 14910 Z= 0.293 Chirality : 0.038 0.134 1632 Planarity : 0.004 0.049 1894 Dihedral : 4.358 15.710 1422 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.46 % Allowed : 13.80 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1300 helix: 0.51 (0.15), residues: 936 sheet: -1.90 (0.66), residues: 68 loop : -2.36 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 235 HIS 0.003 0.001 HIS A 58 PHE 0.014 0.001 PHE B 426 TYR 0.014 0.002 TYR B 26 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8556 (t0) REVERT: A 482 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: B 378 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8579 (t0) REVERT: B 482 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: B 638 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7541 (tm-30) outliers start: 28 outliers final: 19 residues processed: 153 average time/residue: 0.2391 time to fit residues: 53.5775 Evaluate side-chains 138 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 10992 Z= 0.567 Angle : 0.754 6.436 14910 Z= 0.403 Chirality : 0.044 0.141 1632 Planarity : 0.005 0.046 1894 Dihedral : 4.481 18.377 1422 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.66 % Allowed : 15.29 % Favored : 80.05 % 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: 0.07 (0.23), residues: 1300 helix: 0.93 (0.16), residues: 942 sheet: -1.96 (0.59), residues: 76 loop : -2.27 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 235 HIS 0.006 0.001 HIS B 479 PHE 0.026 0.002 PHE A 189 TYR 0.027 0.003 TYR B 279 ARG 0.004 0.001 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 104 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7875 (t0) REVERT: A 203 SER cc_start: 0.8948 (t) cc_final: 0.8497 (p) REVERT: A 482 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: B 173 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7884 (t0) REVERT: B 203 SER cc_start: 0.8954 (t) cc_final: 0.8539 (p) outliers start: 53 outliers final: 33 residues processed: 143 average time/residue: 0.1843 time to fit residues: 41.3030 Evaluate side-chains 133 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 58 HIS B 156 ASN B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10992 Z= 0.167 Angle : 0.539 7.360 14910 Z= 0.281 Chirality : 0.037 0.136 1632 Planarity : 0.004 0.043 1894 Dihedral : 4.186 14.942 1422 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.81 % Allowed : 17.75 % Favored : 79.44 % 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 (0.23), residues: 1300 helix: 1.53 (0.16), residues: 940 sheet: -1.74 (0.68), residues: 68 loop : -2.09 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 235 HIS 0.005 0.001 HIS B 58 PHE 0.020 0.001 PHE B 335 TYR 0.014 0.001 TYR B 26 ARG 0.002 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.8816 (t) cc_final: 0.8405 (p) REVERT: A 482 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: B 203 SER cc_start: 0.8821 (t) cc_final: 0.8415 (p) REVERT: B 575 THR cc_start: 0.9101 (m) cc_final: 0.8811 (p) REVERT: B 638 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7295 (mp0) outliers start: 32 outliers final: 22 residues processed: 145 average time/residue: 0.1980 time to fit residues: 43.4033 Evaluate side-chains 130 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 0.0570 chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10992 Z= 0.349 Angle : 0.607 6.227 14910 Z= 0.319 Chirality : 0.040 0.129 1632 Planarity : 0.004 0.044 1894 Dihedral : 4.136 16.280 1422 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.78 % Allowed : 19.33 % Favored : 76.89 % 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: 0.93 (0.23), residues: 1300 helix: 1.57 (0.16), residues: 942 sheet: -1.67 (0.70), residues: 66 loop : -2.01 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 235 HIS 0.004 0.001 HIS B 479 PHE 0.017 0.002 PHE A 189 TYR 0.016 0.002 TYR B 279 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.8863 (t) cc_final: 0.8425 (p) REVERT: A 378 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8587 (t0) REVERT: A 384 MET cc_start: 0.8715 (tpp) cc_final: 0.8037 (mpp) REVERT: A 482 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: B 203 SER cc_start: 0.8870 (t) cc_final: 0.8435 (p) REVERT: B 378 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8591 (t0) REVERT: B 638 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7324 (mp0) outliers start: 43 outliers final: 32 residues processed: 131 average time/residue: 0.1906 time to fit residues: 38.2111 Evaluate side-chains 135 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10992 Z= 0.230 Angle : 0.556 7.324 14910 Z= 0.290 Chirality : 0.038 0.131 1632 Planarity : 0.004 0.045 1894 Dihedral : 4.076 15.348 1422 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.04 % Allowed : 19.77 % Favored : 76.19 % 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: 1.15 (0.23), residues: 1300 helix: 1.70 (0.16), residues: 940 sheet: -1.39 (0.70), residues: 68 loop : -1.83 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 235 HIS 0.003 0.001 HIS A 265 PHE 0.013 0.001 PHE A 640 TYR 0.014 0.002 TYR B 26 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7832 (t0) REVERT: A 203 SER cc_start: 0.8865 (t) cc_final: 0.8464 (p) REVERT: A 384 MET cc_start: 0.8696 (tpp) cc_final: 0.8037 (mpp) REVERT: A 439 TYR cc_start: 0.7593 (m-80) cc_final: 0.7291 (m-80) REVERT: A 482 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: A 565 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9066 (mp) REVERT: B 203 SER cc_start: 0.8871 (t) cc_final: 0.8467 (p) REVERT: B 565 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9086 (mp) REVERT: B 638 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7284 (mp0) outliers start: 46 outliers final: 37 residues processed: 143 average time/residue: 0.2050 time to fit residues: 44.5918 Evaluate side-chains 143 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.0040 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10992 Z= 0.173 Angle : 0.531 7.282 14910 Z= 0.274 Chirality : 0.037 0.137 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.963 13.474 1422 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.95 % Allowed : 20.83 % Favored : 75.22 % 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: 1.35 (0.23), residues: 1300 helix: 1.86 (0.16), residues: 942 sheet: -1.25 (0.72), residues: 68 loop : -1.83 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 235 HIS 0.002 0.001 HIS A 265 PHE 0.020 0.001 PHE B 335 TYR 0.011 0.001 TYR B 26 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.8861 (t) cc_final: 0.8536 (p) REVERT: A 378 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8492 (t0) REVERT: A 384 MET cc_start: 0.8683 (tpp) cc_final: 0.8067 (mpp) REVERT: A 482 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: A 565 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9047 (mp) REVERT: B 203 SER cc_start: 0.8859 (t) cc_final: 0.8541 (p) REVERT: B 384 MET cc_start: 0.8668 (tpp) cc_final: 0.8088 (mpp) REVERT: B 439 TYR cc_start: 0.7569 (m-80) cc_final: 0.7056 (m-80) REVERT: B 565 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9077 (mp) REVERT: B 638 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7279 (mp0) outliers start: 45 outliers final: 32 residues processed: 153 average time/residue: 0.2090 time to fit residues: 47.4902 Evaluate side-chains 146 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 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 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10992 Z= 0.171 Angle : 0.532 6.820 14910 Z= 0.273 Chirality : 0.037 0.139 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.893 14.067 1422 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.60 % Allowed : 21.27 % Favored : 75.13 % 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: 1.56 (0.24), residues: 1300 helix: 2.01 (0.16), residues: 942 sheet: -1.17 (0.73), residues: 68 loop : -1.73 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 235 HIS 0.002 0.001 HIS A 143 PHE 0.021 0.001 PHE B 335 TYR 0.011 0.001 TYR A 327 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 MET cc_start: 0.8643 (tpp) cc_final: 0.8030 (mpp) REVERT: A 482 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: A 565 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9045 (mp) REVERT: B 378 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8503 (t0) REVERT: B 384 MET cc_start: 0.8675 (tpp) cc_final: 0.8058 (mpp) REVERT: B 565 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9047 (mp) REVERT: B 638 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7472 (tm-30) outliers start: 41 outliers final: 28 residues processed: 154 average time/residue: 0.1896 time to fit residues: 44.3569 Evaluate side-chains 142 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.6980 chunk 121 optimal weight: 0.0010 chunk 71 optimal weight: 0.3980 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 77 optimal weight: 0.0170 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10992 Z= 0.152 Angle : 0.578 17.581 14910 Z= 0.281 Chirality : 0.037 0.157 1632 Planarity : 0.004 0.044 1894 Dihedral : 3.813 15.056 1422 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.64 % Allowed : 22.41 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1300 helix: 2.08 (0.16), residues: 940 sheet: -1.14 (0.73), residues: 68 loop : -1.61 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 235 HIS 0.002 0.000 HIS A 143 PHE 0.022 0.001 PHE B 335 TYR 0.010 0.001 TYR A 327 ARG 0.002 0.000 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8501 (t0) REVERT: A 384 MET cc_start: 0.8629 (tpp) cc_final: 0.7919 (mpp) REVERT: A 437 MET cc_start: 0.9333 (tpp) cc_final: 0.9101 (tpp) REVERT: A 482 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: A 565 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9007 (mp) REVERT: B 384 MET cc_start: 0.8570 (tpp) cc_final: 0.7987 (mpp) REVERT: B 437 MET cc_start: 0.9362 (tpp) cc_final: 0.9030 (tpp) REVERT: B 565 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9025 (mp) REVERT: B 638 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7461 (tm-30) outliers start: 30 outliers final: 19 residues processed: 140 average time/residue: 0.1976 time to fit residues: 41.1965 Evaluate side-chains 132 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10992 Z= 0.250 Angle : 0.604 14.091 14910 Z= 0.299 Chirality : 0.038 0.154 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.775 15.259 1422 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.72 % Allowed : 22.93 % Favored : 74.34 % 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: 1.72 (0.24), residues: 1300 helix: 2.12 (0.16), residues: 942 sheet: -1.15 (0.73), residues: 66 loop : -1.63 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.018 0.001 PHE B 335 TYR 0.011 0.002 TYR B 26 ARG 0.003 0.000 ARG A 710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 MET cc_start: 0.8698 (tpp) cc_final: 0.7958 (mpp) REVERT: A 482 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: A 565 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9058 (mp) REVERT: B 203 SER cc_start: 0.8652 (t) cc_final: 0.8345 (p) REVERT: B 378 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8604 (t0) REVERT: B 384 MET cc_start: 0.8695 (tpp) cc_final: 0.8065 (mpp) REVERT: B 565 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9085 (mp) REVERT: B 638 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7250 (mp0) outliers start: 31 outliers final: 25 residues processed: 135 average time/residue: 0.2024 time to fit residues: 41.8989 Evaluate side-chains 134 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 0.0570 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.078298 restraints weight = 24831.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080597 restraints weight = 13626.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082028 restraints weight = 9672.284| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10992 Z= 0.355 Angle : 0.664 14.241 14910 Z= 0.335 Chirality : 0.040 0.156 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.949 16.406 1422 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.16 % Allowed : 22.67 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1300 helix: 1.95 (0.16), residues: 942 sheet: -1.16 (0.69), residues: 66 loop : -1.79 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 159 HIS 0.004 0.001 HIS B 479 PHE 0.020 0.002 PHE B 379 TYR 0.016 0.002 TYR A 279 ARG 0.002 0.000 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1969.19 seconds wall clock time: 36 minutes 57.49 seconds (2217.49 seconds total)