Starting phenix.real_space_refine on Sun Aug 4 13:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/08_2024/8xry_38611.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/08_2024/8xry_38611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/08_2024/8xry_38611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/08_2024/8xry_38611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/08_2024/8xry_38611.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/08_2024/8xry_38611.cif" } resolution = 3.84 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= 0.008 sd= 0.071 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 36 5.16 5 C 7032 2.51 5 N 1722 2.21 5 O 1826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5308 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 31, 'TRANS': 664} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 167 Chain: "B" Number of atoms: 5308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5308 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 31, 'TRANS': 664} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 167 Time building chain proxies: 6.31, per 1000 atoms: 0.59 Number of scatterers: 10616 At special positions: 0 Unit cell: (90.73, 139.26, 102.335, 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 36 16.00 O 1826 8.00 N 1722 7.00 C 7032 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: 4.06 Conformation dependent library (CDL) restraints added in 2.3 seconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 2 sheets defined 72.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 29 removed outlier: 4.217A pdb=" N ARG A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 78 through 100 removed outlier: 3.658A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.395A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.567A pdb=" N MET A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 184 removed outlier: 3.764A pdb=" N GLY A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 218 Processing helix chain 'A' and resid 233 through 254 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.845A pdb=" N TYR A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 355 through 376 Processing helix chain 'A' and resid 377 through 386 removed outlier: 4.017A pdb=" N ILE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.570A pdb=" N ALA A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 Proline residue: A 418 - end of helix removed outlier: 4.069A pdb=" N PHE A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 469 removed outlier: 4.039A pdb=" N ILE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.690A pdb=" N ILE A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 502 through 523 Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.967A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 removed outlier: 4.224A pdb=" N GLY A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 611 through 638 removed outlier: 4.508A pdb=" N HIS A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 665 removed outlier: 3.558A pdb=" N VAL A 646 " --> pdb=" O TYR A 642 " (cutoff:3.500A) Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.725A pdb=" N GLU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing helix chain 'A' and resid 686 through 694 removed outlier: 4.105A pdb=" N PHE A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.217A pdb=" N ARG B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 100 removed outlier: 3.658A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 4.394A pdb=" N THR B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.568A pdb=" N MET B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 184 removed outlier: 3.764A pdb=" N GLY B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 Processing helix chain 'B' and resid 233 through 254 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.846A pdb=" N TYR B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 325 Processing helix chain 'B' and resid 355 through 376 Processing helix chain 'B' and resid 377 through 386 removed outlier: 4.018A pdb=" N ILE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 392 through 396 Processing helix chain 'B' and resid 401 through 409 removed outlier: 3.570A pdb=" N ALA B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 439 Proline residue: B 418 - end of helix removed outlier: 4.070A pdb=" N PHE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 469 removed outlier: 4.039A pdb=" N ILE B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 484 Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.690A pdb=" N ILE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 502 through 523 Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.967A pdb=" N PHE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 610 removed outlier: 4.224A pdb=" N GLY B 610 " --> pdb=" O GLU B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 610' Processing helix chain 'B' and resid 611 through 638 removed outlier: 4.509A pdb=" N HIS B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 665 removed outlier: 3.558A pdb=" N VAL B 646 " --> pdb=" O TYR B 642 " (cutoff:3.500A) Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.726A pdb=" N GLU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 670' Processing helix chain 'B' and resid 686 through 694 removed outlier: 4.105A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA2, first strand: chain 'B' and resid 228 through 229 672 hydrogen bonds defined for protein. 1944 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: 3.44 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: 1.23 - 1.34: 3211 1.34 - 1.46: 2241 1.46 - 1.58: 5382 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 10892 Sorted by residual: bond pdb=" C LEU B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 1.334 1.348 -0.014 8.40e-03 1.42e+04 2.87e+00 bond pdb=" C LEU A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.334 1.347 -0.013 8.40e-03 1.42e+04 2.52e+00 bond pdb=" C ILE B 397 " pdb=" N PRO B 398 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.22e+00 bond pdb=" C ILE A 397 " pdb=" N PRO A 398 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.17e+00 bond pdb=" CA GLN A 206 " pdb=" C GLN A 206 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.41e-01 ... (remaining 10887 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.86: 310 106.86 - 113.66: 6110 113.66 - 120.45: 4383 120.45 - 127.25: 3937 127.25 - 134.05: 128 Bond angle restraints: 14868 Sorted by residual: angle pdb=" C PRO A 203 " pdb=" N ASP A 204 " pdb=" CA ASP A 204 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 angle pdb=" C PRO B 203 " pdb=" N ASP B 204 " pdb=" CA ASP B 204 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C PRO A 58 " pdb=" N PHE A 59 " pdb=" CA PHE A 59 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C PRO B 58 " pdb=" N PHE B 59 " pdb=" CA PHE B 59 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C LYS B 486 " pdb=" N LEU B 487 " pdb=" CA LEU B 487 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 ... (remaining 14863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 5710 16.33 - 32.66: 558 32.66 - 48.98: 90 48.98 - 65.31: 16 65.31 - 81.64: 2 Dihedral angle restraints: 6376 sinusoidal: 2270 harmonic: 4106 Sorted by residual: dihedral pdb=" CA PHE A 59 " pdb=" C PHE A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual 180.00 146.92 33.08 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA PHE B 59 " pdb=" C PHE B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA GLY B 441 " pdb=" C GLY B 441 " pdb=" N ILE B 442 " pdb=" CA ILE B 442 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1162 0.037 - 0.074: 441 0.074 - 0.111: 140 0.111 - 0.148: 27 0.148 - 0.185: 6 Chirality restraints: 1776 Sorted by residual: chirality pdb=" CA ASP A 204 " pdb=" N ASP A 204 " pdb=" C ASP A 204 " pdb=" CB ASP A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA ASP B 204 " pdb=" N ASP B 204 " pdb=" C ASP B 204 " pdb=" CB ASP B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA PHE A 664 " pdb=" N PHE A 664 " pdb=" C PHE A 664 " pdb=" CB PHE A 664 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 1773 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 202 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 203 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 202 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B 203 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 484 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 485 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.038 5.00e-02 4.00e+02 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2534 2.78 - 3.31: 10899 3.31 - 3.84: 17498 3.84 - 4.37: 18819 4.37 - 4.90: 32469 Nonbonded interactions: 82219 Sorted by model distance: nonbonded pdb=" NH2 ARG A 56 " pdb=" O ALA A 60 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG B 56 " pdb=" O ALA B 60 " model vdw 2.254 3.120 nonbonded pdb=" ND2 ASN A 261 " pdb=" OG SER A 280 " model vdw 2.299 3.120 nonbonded pdb=" OD1 ASP A 562 " pdb=" OH TYR A 586 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASP B 562 " pdb=" OH TYR B 586 " model vdw 2.300 3.040 ... (remaining 82214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.880 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.230 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10892 Z= 0.229 Angle : 0.744 10.558 14868 Z= 0.395 Chirality : 0.044 0.185 1776 Planarity : 0.005 0.070 1826 Dihedral : 12.985 81.641 3712 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.26 (0.24), residues: 1384 helix: 0.98 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -2.50 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 613 HIS 0.005 0.001 HIS A 615 PHE 0.018 0.002 PHE B 376 TYR 0.024 0.002 TYR B 171 ARG 0.002 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.207 Fit side-chains REVERT: A 240 TRP cc_start: 0.9092 (t60) cc_final: 0.8641 (t60) REVERT: A 462 PHE cc_start: 0.7374 (m-10) cc_final: 0.7127 (m-10) REVERT: A 522 SER cc_start: 0.9371 (p) cc_final: 0.9118 (p) REVERT: B 14 PHE cc_start: 0.8836 (t80) cc_final: 0.8592 (t80) REVERT: B 26 TRP cc_start: 0.8555 (t60) cc_final: 0.8331 (t60) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1654 time to fit residues: 44.6570 Evaluate side-chains 139 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 353 ASN B 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10892 Z= 0.246 Angle : 0.697 12.060 14868 Z= 0.348 Chirality : 0.043 0.167 1776 Planarity : 0.005 0.063 1826 Dihedral : 5.239 32.015 1484 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.45 % Favored : 91.40 % Rotamer: Outliers : 1.96 % Allowed : 10.34 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.26 (0.24), residues: 1384 helix: 1.02 (0.18), residues: 912 sheet: None (None), residues: 0 loop : -2.67 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 613 HIS 0.004 0.001 HIS A 615 PHE 0.037 0.002 PHE B 640 TYR 0.016 0.002 TYR B 171 ARG 0.002 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.123 Fit side-chains REVERT: A 113 ASP cc_start: 0.7803 (p0) cc_final: 0.7375 (p0) REVERT: A 198 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: A 240 TRP cc_start: 0.9036 (t60) cc_final: 0.8647 (t60) REVERT: A 519 LEU cc_start: 0.9393 (mm) cc_final: 0.9135 (mp) REVERT: A 522 SER cc_start: 0.9363 (p) cc_final: 0.9103 (p) REVERT: A 642 TYR cc_start: 0.6753 (p90) cc_final: 0.6316 (p90) REVERT: B 14 PHE cc_start: 0.8796 (t80) cc_final: 0.8572 (t80) REVERT: B 113 ASP cc_start: 0.7721 (p0) cc_final: 0.7323 (p0) REVERT: B 522 SER cc_start: 0.9438 (p) cc_final: 0.9232 (p) REVERT: B 690 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7295 (m-10) outliers start: 21 outliers final: 14 residues processed: 174 average time/residue: 0.1660 time to fit residues: 45.0615 Evaluate side-chains 159 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 50.0000 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10892 Z= 0.217 Angle : 0.655 11.064 14868 Z= 0.324 Chirality : 0.042 0.136 1776 Planarity : 0.005 0.064 1826 Dihedral : 5.083 31.460 1484 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.33 % Allowed : 14.71 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.20 (0.24), residues: 1384 helix: 1.04 (0.18), residues: 916 sheet: -2.27 (1.11), residues: 20 loop : -2.60 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.005 0.001 HIS A 615 PHE 0.029 0.001 PHE B 513 TYR 0.030 0.001 TYR B 171 ARG 0.002 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8693 (tt) cc_final: 0.8483 (tt) REVERT: A 113 ASP cc_start: 0.7682 (p0) cc_final: 0.7256 (p0) REVERT: A 240 TRP cc_start: 0.9032 (t60) cc_final: 0.8542 (t60) REVERT: A 642 TYR cc_start: 0.6694 (p90) cc_final: 0.6400 (p90) REVERT: B 14 PHE cc_start: 0.8862 (t80) cc_final: 0.8649 (t80) REVERT: B 113 ASP cc_start: 0.7732 (p0) cc_final: 0.7262 (p0) REVERT: B 522 SER cc_start: 0.9382 (p) cc_final: 0.9177 (p) REVERT: B 619 ARG cc_start: 0.7974 (mpt90) cc_final: 0.7689 (mmt180) REVERT: B 690 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7213 (m-10) outliers start: 25 outliers final: 16 residues processed: 176 average time/residue: 0.1798 time to fit residues: 48.8013 Evaluate side-chains 160 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.0010 chunk 94 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 261 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.193 Angle : 0.633 10.591 14868 Z= 0.313 Chirality : 0.041 0.167 1776 Planarity : 0.005 0.062 1826 Dihedral : 4.943 31.458 1484 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.35 % Allowed : 16.67 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.14 (0.24), residues: 1384 helix: 1.10 (0.18), residues: 916 sheet: -1.75 (1.22), residues: 20 loop : -2.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 613 HIS 0.005 0.001 HIS A 615 PHE 0.029 0.001 PHE A 513 TYR 0.029 0.001 TYR B 171 ARG 0.001 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8598 (tt) cc_final: 0.8394 (tt) REVERT: A 29 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7736 (mtt-85) REVERT: A 113 ASP cc_start: 0.7593 (p0) cc_final: 0.7173 (p0) REVERT: A 240 TRP cc_start: 0.9028 (t60) cc_final: 0.8508 (t60) REVERT: A 519 LEU cc_start: 0.9485 (mm) cc_final: 0.9228 (mp) REVERT: A 642 TYR cc_start: 0.6599 (p90) cc_final: 0.6264 (p90) REVERT: B 14 PHE cc_start: 0.8873 (t80) cc_final: 0.8665 (t80) REVERT: B 521 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9031 (tt) REVERT: B 619 ARG cc_start: 0.7926 (mpt90) cc_final: 0.7620 (mmt180) REVERT: B 690 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7154 (m-10) outliers start: 36 outliers final: 22 residues processed: 173 average time/residue: 0.1853 time to fit residues: 48.2149 Evaluate side-chains 159 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.210 Angle : 0.656 12.964 14868 Z= 0.317 Chirality : 0.041 0.168 1776 Planarity : 0.005 0.067 1826 Dihedral : 4.854 31.240 1484 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.98 % Allowed : 19.09 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.06 (0.24), residues: 1384 helix: 1.15 (0.18), residues: 916 sheet: -1.35 (1.27), residues: 20 loop : -2.59 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 548 HIS 0.005 0.001 HIS B 615 PHE 0.027 0.001 PHE A 513 TYR 0.036 0.001 TYR B 171 ARG 0.002 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7799 (mtt-85) REVERT: A 113 ASP cc_start: 0.7595 (p0) cc_final: 0.7181 (p0) REVERT: A 232 GLU cc_start: 0.6622 (pm20) cc_final: 0.6222 (pm20) REVERT: A 240 TRP cc_start: 0.8994 (t60) cc_final: 0.8464 (t60) REVERT: A 519 LEU cc_start: 0.9518 (mm) cc_final: 0.9199 (mp) REVERT: A 642 TYR cc_start: 0.6603 (p90) cc_final: 0.6339 (p90) REVERT: B 14 PHE cc_start: 0.8881 (t80) cc_final: 0.8654 (t80) REVERT: B 521 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9027 (tt) REVERT: B 619 ARG cc_start: 0.7963 (mpt90) cc_final: 0.7638 (mmt180) REVERT: B 641 PHE cc_start: 0.7873 (m-80) cc_final: 0.7655 (m-10) outliers start: 32 outliers final: 24 residues processed: 173 average time/residue: 0.1886 time to fit residues: 48.7381 Evaluate side-chains 160 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.0010 chunk 133 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10892 Z= 0.224 Angle : 0.650 11.481 14868 Z= 0.315 Chirality : 0.042 0.164 1776 Planarity : 0.005 0.072 1826 Dihedral : 4.797 31.382 1484 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.72 % Allowed : 19.93 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.24), residues: 1384 helix: 1.18 (0.18), residues: 918 sheet: -1.11 (1.30), residues: 20 loop : -2.52 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 548 HIS 0.005 0.001 HIS B 615 PHE 0.027 0.001 PHE A 513 TYR 0.011 0.001 TYR B 220 ARG 0.002 0.000 ARG B 595 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7726 (mtt180) REVERT: A 63 ARG cc_start: 0.7400 (ttm110) cc_final: 0.7132 (ttm110) REVERT: A 113 ASP cc_start: 0.7563 (p0) cc_final: 0.7205 (p0) REVERT: A 240 TRP cc_start: 0.8995 (t60) cc_final: 0.8440 (t60) REVERT: A 570 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8433 (m-10) REVERT: A 642 TYR cc_start: 0.6602 (p90) cc_final: 0.6347 (p90) REVERT: B 14 PHE cc_start: 0.8824 (t80) cc_final: 0.8619 (t80) REVERT: B 29 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7616 (mtt-85) REVERT: B 520 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8492 (tm-30) outliers start: 40 outliers final: 32 residues processed: 176 average time/residue: 0.1998 time to fit residues: 52.1472 Evaluate side-chains 174 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.207 Angle : 0.652 10.898 14868 Z= 0.313 Chirality : 0.041 0.159 1776 Planarity : 0.005 0.072 1826 Dihedral : 4.739 31.268 1484 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.35 % Allowed : 20.95 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.12 (0.24), residues: 1384 helix: 1.22 (0.18), residues: 926 sheet: -0.91 (1.34), residues: 20 loop : -2.43 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 548 HIS 0.005 0.001 HIS B 615 PHE 0.027 0.001 PHE A 513 TYR 0.011 0.001 TYR B 220 ARG 0.002 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7735 (mtt180) REVERT: A 63 ARG cc_start: 0.7430 (ttm110) cc_final: 0.7154 (ttm110) REVERT: A 113 ASP cc_start: 0.7555 (p0) cc_final: 0.7224 (p0) REVERT: A 378 MET cc_start: 0.7268 (mmm) cc_final: 0.6633 (mtp) REVERT: A 642 TYR cc_start: 0.6583 (p90) cc_final: 0.6320 (p90) REVERT: B 14 PHE cc_start: 0.8817 (t80) cc_final: 0.8603 (t80) REVERT: B 29 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7606 (mtt-85) REVERT: B 520 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8527 (tm-30) REVERT: B 690 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7388 (m-10) outliers start: 36 outliers final: 27 residues processed: 177 average time/residue: 0.1944 time to fit residues: 50.8363 Evaluate side-chains 169 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.215 Angle : 0.661 10.407 14868 Z= 0.315 Chirality : 0.041 0.159 1776 Planarity : 0.005 0.076 1826 Dihedral : 4.710 32.382 1484 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.72 % Allowed : 21.04 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.15 (0.25), residues: 1384 helix: 1.23 (0.18), residues: 928 sheet: -1.33 (1.27), residues: 22 loop : -2.39 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 548 HIS 0.005 0.001 HIS B 615 PHE 0.020 0.001 PHE B 640 TYR 0.011 0.001 TYR B 220 ARG 0.002 0.000 ARG B 595 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7709 (mtt180) REVERT: A 63 ARG cc_start: 0.7431 (ttm110) cc_final: 0.7159 (ttm110) REVERT: A 113 ASP cc_start: 0.7521 (p0) cc_final: 0.7210 (p0) REVERT: A 519 LEU cc_start: 0.9532 (mm) cc_final: 0.9142 (mp) REVERT: A 642 TYR cc_start: 0.6532 (p90) cc_final: 0.6269 (p90) REVERT: B 14 PHE cc_start: 0.8801 (t80) cc_final: 0.8590 (t80) REVERT: B 56 ARG cc_start: 0.7685 (tpt90) cc_final: 0.6923 (mmm160) REVERT: B 378 MET cc_start: 0.7029 (mmm) cc_final: 0.6703 (mmm) REVERT: B 489 MET cc_start: 0.5583 (ppp) cc_final: 0.5006 (ppp) REVERT: B 619 ARG cc_start: 0.7975 (mpt90) cc_final: 0.7639 (mmt180) REVERT: B 690 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7289 (m-10) outliers start: 40 outliers final: 31 residues processed: 171 average time/residue: 0.2164 time to fit residues: 54.8612 Evaluate side-chains 170 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10892 Z= 0.228 Angle : 0.665 10.692 14868 Z= 0.320 Chirality : 0.042 0.158 1776 Planarity : 0.005 0.078 1826 Dihedral : 4.695 31.798 1484 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.07 % Allowed : 21.60 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.17 (0.25), residues: 1384 helix: 1.23 (0.18), residues: 928 sheet: -1.29 (1.26), residues: 22 loop : -2.35 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 548 HIS 0.005 0.001 HIS B 615 PHE 0.019 0.001 PHE B 690 TYR 0.010 0.001 TYR A 364 ARG 0.006 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7698 (mtt180) REVERT: A 63 ARG cc_start: 0.7439 (ttm110) cc_final: 0.7167 (ttm110) REVERT: A 113 ASP cc_start: 0.7533 (p0) cc_final: 0.7217 (p0) REVERT: A 519 LEU cc_start: 0.9552 (mm) cc_final: 0.9336 (mp) REVERT: A 642 TYR cc_start: 0.6539 (p90) cc_final: 0.6211 (p90) REVERT: B 14 PHE cc_start: 0.8803 (t80) cc_final: 0.8582 (t80) REVERT: B 378 MET cc_start: 0.7070 (mmm) cc_final: 0.6788 (mmm) REVERT: B 579 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 619 ARG cc_start: 0.8011 (mpt90) cc_final: 0.7663 (mmt180) REVERT: B 690 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7306 (m-10) outliers start: 33 outliers final: 29 residues processed: 163 average time/residue: 0.2065 time to fit residues: 50.1213 Evaluate side-chains 168 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 0.1980 chunk 109 optimal weight: 40.0000 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 116 optimal weight: 30.0000 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10892 Z= 0.169 Angle : 0.658 11.924 14868 Z= 0.310 Chirality : 0.041 0.154 1776 Planarity : 0.005 0.079 1826 Dihedral : 4.555 30.794 1484 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.70 % Allowed : 22.16 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.32 (0.25), residues: 1384 helix: 1.33 (0.18), residues: 928 sheet: -0.81 (1.34), residues: 22 loop : -2.27 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 548 HIS 0.006 0.001 HIS B 615 PHE 0.019 0.001 PHE B 640 TYR 0.009 0.001 TYR B 220 ARG 0.002 0.000 ARG B 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7757 (mtt180) REVERT: A 63 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7141 (ttm110) REVERT: A 113 ASP cc_start: 0.7446 (p0) cc_final: 0.7157 (p0) REVERT: A 183 MET cc_start: 0.8118 (tpp) cc_final: 0.7868 (tpp) REVERT: A 519 LEU cc_start: 0.9529 (mm) cc_final: 0.9170 (mp) REVERT: A 548 TRP cc_start: 0.8972 (p-90) cc_final: 0.8645 (p-90) REVERT: A 571 CYS cc_start: 0.8086 (m) cc_final: 0.7331 (t) REVERT: A 642 TYR cc_start: 0.6490 (p90) cc_final: 0.6268 (p90) REVERT: A 661 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7832 (ttm-80) REVERT: A 690 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: B 14 PHE cc_start: 0.8757 (t80) cc_final: 0.8535 (t80) REVERT: B 183 MET cc_start: 0.7912 (tpp) cc_final: 0.7632 (tpp) REVERT: B 378 MET cc_start: 0.7181 (mmm) cc_final: 0.6937 (mmm) REVERT: B 579 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8314 (tt) REVERT: B 690 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7419 (m-10) outliers start: 29 outliers final: 23 residues processed: 167 average time/residue: 0.2053 time to fit residues: 49.9006 Evaluate side-chains 166 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 690 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.169868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125687 restraints weight = 14864.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126176 restraints weight = 15064.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127755 restraints weight = 11770.484| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10892 Z= 0.212 Angle : 0.659 11.662 14868 Z= 0.312 Chirality : 0.041 0.152 1776 Planarity : 0.005 0.080 1826 Dihedral : 4.551 31.115 1484 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.51 % Allowed : 21.97 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.35 (0.25), residues: 1384 helix: 1.35 (0.18), residues: 930 sheet: -0.74 (1.34), residues: 22 loop : -2.26 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 548 HIS 0.002 0.000 HIS A 615 PHE 0.018 0.001 PHE B 690 TYR 0.017 0.001 TYR A 220 ARG 0.002 0.000 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.16 seconds wall clock time: 36 minutes 22.83 seconds (2182.83 seconds total)