Starting phenix.real_space_refine on Sat Jul 20 10:09:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/07_2024/8xry_38611.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/07_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_38611/07_2024/8xry_38611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/07_2024/8xry_38611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/07_2024/8xry_38611.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xry_38611/07_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-5388/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: 5.97, per 1000 atoms: 0.56 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: 4.32 Conformation dependent library (CDL) restraints added in 1.9 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: 1.10 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: 3.17 Time building geometry restraints manager: 4.76 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 2.520 nonbonded pdb=" NH2 ARG B 56 " pdb=" O ALA B 60 " model vdw 2.254 2.520 nonbonded pdb=" ND2 ASN A 261 " pdb=" OG SER A 280 " model vdw 2.299 2.520 nonbonded pdb=" OD1 ASP A 562 " pdb=" OH TYR A 586 " model vdw 2.299 2.440 nonbonded pdb=" OD1 ASP B 562 " pdb=" OH TYR B 586 " model vdw 2.300 2.440 ... (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 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: 2.240 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.530 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- 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 : 1.192 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: 0.1732 time to fit residues: 47.2695 Evaluate side-chains 139 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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: 9.9990 chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 chunk 108 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10892 Z= 0.199 Angle : 0.671 11.866 14868 Z= 0.331 Chirality : 0.042 0.161 1776 Planarity : 0.005 0.063 1826 Dihedral : 5.177 32.887 1484 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.89 % Favored : 90.97 % Rotamer: Outliers : 1.77 % Allowed : 10.43 % Favored : 87.80 % 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: -0.21 (0.24), residues: 1384 helix: 1.08 (0.18), residues: 912 sheet: None (None), residues: 0 loop : -2.69 (0.29), residues: 472 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 0.037 0.002 PHE B 640 TYR 0.020 0.001 TYR B 693 ARG 0.001 0.000 ARG A 691 *********************** 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 168 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.107 Fit side-chains REVERT: A 240 TRP cc_start: 0.9071 (t60) cc_final: 0.8591 (t60) REVERT: A 522 SER cc_start: 0.9403 (p) cc_final: 0.9141 (p) REVERT: A 642 TYR cc_start: 0.6719 (p90) cc_final: 0.6274 (p90) REVERT: B 14 PHE cc_start: 0.8827 (t80) cc_final: 0.8608 (t80) REVERT: B 690 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7405 (m-10) outliers start: 19 outliers final: 16 residues processed: 161 average time/residue: 0.1620 time to fit residues: 41.1594 Evaluate side-chains 148 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 198 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 375 LEU 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 198 ASP 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: 40.0000 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 42 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10892 Z= 0.176 Angle : 0.625 10.408 14868 Z= 0.308 Chirality : 0.041 0.162 1776 Planarity : 0.005 0.064 1826 Dihedral : 4.941 32.421 1484 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.09 % Favored : 91.76 % Rotamer: Outliers : 2.14 % Allowed : 14.43 % Favored : 83.43 % 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: -0.06 (0.24), residues: 1384 helix: 1.21 (0.18), residues: 904 sheet: -1.99 (1.17), residues: 20 loop : -2.59 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 61 HIS 0.005 0.001 HIS A 615 PHE 0.032 0.001 PHE A 513 TYR 0.029 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 171 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.174 Fit side-chains REVERT: A 102 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 240 TRP cc_start: 0.9052 (t60) cc_final: 0.8549 (t60) REVERT: A 520 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8231 (tm-30) REVERT: A 642 TYR cc_start: 0.6648 (p90) cc_final: 0.6328 (p90) REVERT: B 14 PHE cc_start: 0.8893 (t80) cc_final: 0.8661 (t80) REVERT: B 102 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7999 (tp) REVERT: B 690 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7198 (m-10) outliers start: 23 outliers final: 13 residues processed: 163 average time/residue: 0.1647 time to fit residues: 42.5069 Evaluate side-chains 145 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 198 ASP 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 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 198 ASP Chi-restraints excluded: chain B residue 309 THR 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: 0.0270 chunk 94 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10892 Z= 0.221 Angle : 0.645 12.242 14868 Z= 0.313 Chirality : 0.041 0.159 1776 Planarity : 0.005 0.064 1826 Dihedral : 4.860 33.265 1484 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.60 % Favored : 91.26 % Rotamer: Outliers : 3.35 % Allowed : 17.32 % Favored : 79.33 % 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: -0.01 (0.24), residues: 1384 helix: 1.24 (0.18), residues: 904 sheet: -1.58 (1.25), residues: 20 loop : -2.58 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 61 HIS 0.004 0.001 HIS B 615 PHE 0.028 0.001 PHE A 513 TYR 0.034 0.001 TYR B 171 ARG 0.002 0.000 ARG A 595 *********************** 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 168 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.166 Fit side-chains REVERT: A 226 ARG cc_start: 0.5873 (ptm160) cc_final: 0.5639 (ptm160) REVERT: A 240 TRP cc_start: 0.9077 (t60) cc_final: 0.8588 (t60) REVERT: A 520 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8290 (tm-30) REVERT: A 548 TRP cc_start: 0.8568 (p-90) cc_final: 0.8295 (p-90) REVERT: A 642 TYR cc_start: 0.6644 (p90) cc_final: 0.6354 (p90) REVERT: B 14 PHE cc_start: 0.8869 (t80) cc_final: 0.8638 (t80) REVERT: B 690 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7258 (m-10) outliers start: 36 outliers final: 26 residues processed: 156 average time/residue: 0.1705 time to fit residues: 41.1516 Evaluate side-chains 151 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 190 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 332 MET 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 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 187 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 462 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10892 Z= 0.251 Angle : 0.653 12.076 14868 Z= 0.317 Chirality : 0.042 0.161 1776 Planarity : 0.004 0.056 1826 Dihedral : 4.858 33.754 1484 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.24 % Favored : 91.62 % Rotamer: Outliers : 3.17 % Allowed : 19.18 % Favored : 77.65 % 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: 0.05 (0.24), residues: 1384 helix: 1.23 (0.18), residues: 914 sheet: -1.45 (1.25), residues: 20 loop : -2.51 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 548 HIS 0.004 0.001 HIS A 615 PHE 0.026 0.001 PHE A 513 TYR 0.039 0.001 TYR B 171 ARG 0.002 0.000 ARG B 595 *********************** 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 165 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 1.161 Fit side-chains REVERT: A 29 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7764 (mtt180) REVERT: A 226 ARG cc_start: 0.6010 (ptm160) cc_final: 0.5800 (ptm160) REVERT: A 240 TRP cc_start: 0.9048 (t60) cc_final: 0.8560 (t60) REVERT: A 642 TYR cc_start: 0.6627 (p90) cc_final: 0.6336 (p90) REVERT: B 14 PHE cc_start: 0.8801 (t80) cc_final: 0.8591 (t80) outliers start: 34 outliers final: 22 residues processed: 151 average time/residue: 0.1826 time to fit residues: 41.8269 Evaluate side-chains 147 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 309 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 506 LEU 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 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 309 THR Chi-restraints excluded: chain B residue 462 PHE 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: 0.0060 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10892 Z= 0.261 Angle : 0.664 13.139 14868 Z= 0.319 Chirality : 0.042 0.163 1776 Planarity : 0.004 0.053 1826 Dihedral : 4.840 33.998 1484 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.24 % Favored : 91.62 % Rotamer: Outliers : 3.82 % Allowed : 20.11 % Favored : 76.07 % 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: 0.08 (0.25), residues: 1384 helix: 1.23 (0.18), residues: 916 sheet: -1.25 (1.27), residues: 20 loop : -2.48 (0.31), residues: 448 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 0.026 0.001 PHE A 513 TYR 0.014 0.001 TYR A 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 173 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.163 Fit side-chains REVERT: A 29 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7840 (mtt-85) REVERT: A 63 ARG cc_start: 0.7408 (ttm110) cc_final: 0.7141 (ttm110) REVERT: A 240 TRP cc_start: 0.9048 (t60) cc_final: 0.8556 (t60) REVERT: A 571 CYS cc_start: 0.8461 (m) cc_final: 0.7435 (t) REVERT: A 642 TYR cc_start: 0.6570 (p90) cc_final: 0.6225 (p90) REVERT: B 14 PHE cc_start: 0.8756 (t80) cc_final: 0.8538 (t80) REVERT: B 690 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7320 (m-10) outliers start: 41 outliers final: 31 residues processed: 159 average time/residue: 0.1766 time to fit residues: 42.6437 Evaluate side-chains 160 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 190 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 332 MET 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 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 309 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 521 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 81 optimal weight: 0.0170 chunk 61 optimal weight: 0.0470 chunk 82 optimal weight: 0.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 670 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10892 Z= 0.161 Angle : 0.628 11.973 14868 Z= 0.298 Chirality : 0.040 0.160 1776 Planarity : 0.004 0.051 1826 Dihedral : 4.658 33.103 1484 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.20 % Rotamer: Outliers : 2.98 % Allowed : 21.23 % Favored : 75.79 % 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: 0.27 (0.25), residues: 1384 helix: 1.36 (0.18), residues: 914 sheet: -1.17 (1.32), residues: 22 loop : -2.33 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 548 HIS 0.005 0.001 HIS B 615 PHE 0.023 0.001 PHE A 513 TYR 0.012 0.001 TYR A 220 ARG 0.002 0.000 ARG A 226 *********************** 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 169 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.118 Fit side-chains REVERT: A 63 ARG cc_start: 0.7421 (ttm110) cc_final: 0.7146 (ttm110) REVERT: A 240 TRP cc_start: 0.9043 (t60) cc_final: 0.8511 (t60) REVERT: A 571 CYS cc_start: 0.8046 (m) cc_final: 0.7215 (t) REVERT: A 642 TYR cc_start: 0.6535 (p90) cc_final: 0.6245 (p90) REVERT: B 14 PHE cc_start: 0.8760 (t80) cc_final: 0.8524 (t80) REVERT: B 378 MET cc_start: 0.7113 (mmm) cc_final: 0.6783 (mmm) REVERT: B 690 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7258 (m-10) outliers start: 32 outliers final: 22 residues processed: 161 average time/residue: 0.1884 time to fit residues: 45.9015 Evaluate side-chains 144 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 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 462 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 601 VAL 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: 20.0000 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10892 Z= 0.300 Angle : 0.667 10.020 14868 Z= 0.323 Chirality : 0.042 0.165 1776 Planarity : 0.004 0.051 1826 Dihedral : 4.762 34.432 1484 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.02 % Favored : 91.84 % Rotamer: Outliers : 2.70 % Allowed : 21.88 % Favored : 75.42 % 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: 0.17 (0.25), residues: 1384 helix: 1.24 (0.18), residues: 926 sheet: -1.46 (1.26), residues: 22 loop : -2.36 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 548 HIS 0.004 0.001 HIS A 615 PHE 0.019 0.001 PHE B 690 TYR 0.013 0.001 TYR A 220 ARG 0.009 0.000 ARG B 619 *********************** 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 158 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.147 Fit side-chains REVERT: A 63 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7179 (ttm110) REVERT: A 642 TYR cc_start: 0.6726 (p90) cc_final: 0.6463 (p90) REVERT: B 14 PHE cc_start: 0.8677 (t80) cc_final: 0.8456 (t80) REVERT: B 378 MET cc_start: 0.7221 (mmm) cc_final: 0.6877 (mmm) REVERT: B 690 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7405 (m-10) outliers start: 29 outliers final: 22 residues processed: 151 average time/residue: 0.1730 time to fit residues: 40.3624 Evaluate side-chains 149 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 190 GLU Chi-restraints excluded: chain A residue 250 LEU 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 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 330 CYS Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 601 VAL 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: 0.8980 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 53 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 38 optimal weight: 0.0980 chunk 112 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10892 Z= 0.170 Angle : 0.640 10.199 14868 Z= 0.303 Chirality : 0.041 0.153 1776 Planarity : 0.004 0.051 1826 Dihedral : 4.638 33.281 1484 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.44 % Favored : 92.41 % Rotamer: Outliers : 2.42 % Allowed : 22.35 % Favored : 75.23 % 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: 0.31 (0.25), residues: 1384 helix: 1.33 (0.18), residues: 928 sheet: -1.04 (1.30), residues: 22 loop : -2.30 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 548 HIS 0.004 0.001 HIS A 615 PHE 0.017 0.001 PHE B 690 TYR 0.011 0.001 TYR A 220 ARG 0.007 0.000 ARG B 619 *********************** 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 157 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.042 Fit side-chains REVERT: A 63 ARG cc_start: 0.7374 (ttm110) cc_final: 0.7131 (ttm110) REVERT: A 378 MET cc_start: 0.7050 (mmm) cc_final: 0.6568 (mtp) REVERT: A 571 CYS cc_start: 0.8047 (m) cc_final: 0.7338 (t) REVERT: A 642 TYR cc_start: 0.6519 (p90) cc_final: 0.6232 (p90) REVERT: B 14 PHE cc_start: 0.8706 (t80) cc_final: 0.8482 (t80) REVERT: B 378 MET cc_start: 0.7104 (mmm) cc_final: 0.6853 (mmm) REVERT: B 690 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7328 (m-10) outliers start: 26 outliers final: 17 residues processed: 147 average time/residue: 0.1758 time to fit residues: 39.5601 Evaluate side-chains 144 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 428 MET 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 690 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 601 VAL 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: 0.0170 chunk 62 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10892 Z= 0.175 Angle : 0.647 14.322 14868 Z= 0.304 Chirality : 0.040 0.157 1776 Planarity : 0.004 0.051 1826 Dihedral : 4.554 33.322 1484 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.23 % Allowed : 23.09 % Favored : 74.67 % 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: 0.44 (0.25), residues: 1384 helix: 1.45 (0.18), residues: 916 sheet: -0.76 (1.32), residues: 22 loop : -2.19 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 548 HIS 0.004 0.000 HIS A 615 PHE 0.017 0.001 PHE B 690 TYR 0.011 0.001 TYR A 220 ARG 0.007 0.000 ARG B 619 ********************** 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 149 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.191 Fit side-chains REVERT: A 63 ARG cc_start: 0.7421 (ttm110) cc_final: 0.7170 (ttm110) REVERT: A 378 MET cc_start: 0.7085 (mmm) cc_final: 0.6411 (mtp) REVERT: A 548 TRP cc_start: 0.8922 (p-90) cc_final: 0.8675 (p-90) REVERT: A 571 CYS cc_start: 0.8029 (m) cc_final: 0.7300 (t) REVERT: A 642 TYR cc_start: 0.6621 (p90) cc_final: 0.6338 (p90) REVERT: B 14 PHE cc_start: 0.8678 (t80) cc_final: 0.8460 (t80) REVERT: B 378 MET cc_start: 0.7268 (mmm) cc_final: 0.6994 (mmm) REVERT: B 520 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8533 (tm-30) REVERT: B 521 LEU cc_start: 0.9397 (tt) cc_final: 0.9186 (tt) REVERT: B 690 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7287 (m-10) outliers start: 24 outliers final: 19 residues processed: 142 average time/residue: 0.1806 time to fit residues: 39.4231 Evaluate side-chains 144 residues out of total 1210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 428 MET 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 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 462 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 601 VAL 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: 1.9990 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 50.0000 chunk 45 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 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 = 0.3813 r_free = 0.3813 target = 0.162811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113876 restraints weight = 16045.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.109796 restraints weight = 16716.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.110399 restraints weight = 15709.916| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10892 Z= 0.242 Angle : 0.671 13.291 14868 Z= 0.316 Chirality : 0.042 0.160 1776 Planarity : 0.004 0.052 1826 Dihedral : 4.632 34.085 1484 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.66 % Favored : 92.20 % Rotamer: Outliers : 2.14 % Allowed : 23.46 % Favored : 74.39 % 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: 0.41 (0.25), residues: 1384 helix: 1.42 (0.18), residues: 916 sheet: -1.14 (1.27), residues: 22 loop : -2.17 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 548 HIS 0.004 0.001 HIS A 615 PHE 0.018 0.001 PHE B 690 TYR 0.012 0.001 TYR A 220 ARG 0.008 0.000 ARG B 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.15 seconds wall clock time: 35 minutes 6.33 seconds (2106.33 seconds total)