Starting phenix.real_space_refine on Tue Jun 25 01:09:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/06_2024/7mgw_23830_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/06_2024/7mgw_23830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/06_2024/7mgw_23830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/06_2024/7mgw_23830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/06_2024/7mgw_23830_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/06_2024/7mgw_23830_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4140 2.51 5 N 964 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 87": "OD1" <-> "OD2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6223 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 160 Unusual residues: {' CL': 1, 'CLR': 1, 'D10': 1, 'D12': 4, 'HP6': 6, 'LNK': 1, 'SRO': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Time building chain proxies: 5.53, per 1000 atoms: 0.89 Number of scatterers: 6223 At special positions: 0 Unit cell: (69.336, 73.224, 121.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 1084 8.00 N 964 7.00 C 4140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 4 sheets defined 48.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 112 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 119 through 143 removed outlier: 4.055A pdb=" N THR A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE A 130 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 156 through 191 removed outlier: 3.598A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 272 removed outlier: 4.364A pdb=" N LYS A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.642A pdb=" N VAL A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 357 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 403 through 416 removed outlier: 4.119A pdb=" N LEU A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 453 removed outlier: 3.807A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 460 removed outlier: 4.511A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 481 removed outlier: 3.852A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 518 through 529 removed outlier: 4.432A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 No H-bonds generated for 'chain 'A' and resid 537 through 540' Processing helix chain 'A' and resid 544 through 558 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 587 through 599 Processing helix chain 'A' and resid 604 through 611 Processing sheet with id= A, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.515A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.000A pdb=" N ASP B 76 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.616A pdb=" N ALA C 39 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS C 43 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 109 through 113 removed outlier: 4.054A pdb=" N TRP C 59 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 72 " --> pdb=" O TRP C 59 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN C 61 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU C 70 " --> pdb=" O GLN C 61 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 624 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: 1.73 Time building geometry restraints manager: 4.16 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: 1816 1.34 - 1.46: 1680 1.46 - 1.58: 2849 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6394 Sorted by residual: bond pdb=" CD1 SRO A 712 " pdb=" NE1 SRO A 712 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" CD1 SRO A 715 " pdb=" NE1 SRO A 715 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" CD2 SRO A 712 " pdb=" CE2 SRO A 712 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CD2 SRO A 715 " pdb=" CE2 SRO A 715 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" CB SRO A 715 " pdb=" CG SRO A 715 " ideal model delta sigma weight residual 1.498 1.527 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 6389 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.22: 196 107.22 - 113.91: 3540 113.91 - 120.61: 2581 120.61 - 127.30: 2264 127.30 - 134.00: 84 Bond angle restraints: 8665 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 132.04 -10.34 1.80e+00 3.09e-01 3.30e+01 angle pdb=" C LEU A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 121.65 119.11 2.54 1.01e+00 9.80e-01 6.34e+00 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.60 118.96 -3.36 1.48e+00 4.57e-01 5.16e+00 angle pdb=" C20 CLR A 716 " pdb=" C22 CLR A 716 " pdb=" C23 CLR A 716 " ideal model delta sigma weight residual 115.57 109.14 6.43 3.00e+00 1.11e-01 4.59e+00 angle pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" C VAL A 236 " ideal model delta sigma weight residual 113.39 110.26 3.13 1.47e+00 4.63e-01 4.53e+00 ... (remaining 8660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 3447 19.03 - 38.06: 230 38.06 - 57.09: 37 57.09 - 76.11: 5 76.11 - 95.14: 10 Dihedral angle restraints: 3729 sinusoidal: 1529 harmonic: 2200 Sorted by residual: dihedral pdb=" C2 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" C5 NAG D 1 " ideal model delta sinusoidal sigma weight residual 53.78 -41.36 95.14 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" C2 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sinusoidal sigma weight residual 175.11 81.72 93.39 1 3.00e+01 1.11e-03 1.13e+01 dihedral pdb=" C5 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O3 NAG D 1 " ideal model delta sinusoidal sigma weight residual -174.13 -81.26 -92.87 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 869 0.068 - 0.137: 74 0.137 - 0.205: 2 0.205 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.95e+01 chirality pdb=" C14 CLR A 716 " pdb=" C13 CLR A 716 " pdb=" C15 CLR A 716 " pdb=" C8 CLR A 716 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C9 CLR A 716 " pdb=" C10 CLR A 716 " pdb=" C11 CLR A 716 " pdb=" C8 CLR A 716 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 945 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 570 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 571 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 100 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO C 101 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 590 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " 0.015 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1879 2.81 - 3.34: 5909 3.34 - 3.86: 10613 3.86 - 4.38: 11466 4.38 - 4.90: 19848 Nonbonded interactions: 49715 Sorted by model distance: nonbonded pdb=" OG1 THR B 106 " pdb=" OD1 ASP B 109 " model vdw 2.292 2.440 nonbonded pdb=" O ILE A 108 " pdb=" ND2 ASN A 112 " model vdw 2.297 2.520 nonbonded pdb=" OG SER C 76 " pdb=" OD1 ASN C 77 " model vdw 2.310 2.440 nonbonded pdb=" OG SER C 55 " pdb=" O ALA C 74 " model vdw 2.313 2.440 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.323 2.440 ... (remaining 49710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 11.310 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: 13.010 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.700 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5007 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 : 0.003 0.053 6394 Z= 0.159 Angle : 0.636 10.336 8665 Z= 0.301 Chirality : 0.041 0.341 948 Planarity : 0.003 0.031 1049 Dihedral : 13.533 95.142 2324 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.40 % Allowed : 9.66 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.28), residues: 759 helix: -0.76 (0.23), residues: 354 sheet: -1.78 (0.51), residues: 93 loop : -2.62 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 317 HIS 0.001 0.000 HIS A 143 PHE 0.015 0.001 PHE A 474 TYR 0.009 0.000 TYR A 176 ARG 0.001 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.689 Fit side-chains REVERT: A 144 ARG cc_start: 0.6293 (mtm110) cc_final: 0.6074 (ttm110) REVERT: A 145 ASN cc_start: 0.6109 (t0) cc_final: 0.5464 (t0) REVERT: A 243 LYS cc_start: 0.7231 (mtmm) cc_final: 0.7008 (mmtm) REVERT: A 267 TYR cc_start: 0.5156 (t80) cc_final: 0.4873 (t80) REVERT: A 370 MET cc_start: 0.6126 (mmp) cc_final: 0.4205 (ttm) REVERT: A 391 ASN cc_start: 0.7447 (t0) cc_final: 0.7161 (t0) REVERT: A 430 MET cc_start: 0.6276 (ttm) cc_final: 0.6050 (tmm) REVERT: A 466 VAL cc_start: 0.3864 (p) cc_final: 0.3450 (t) REVERT: A 508 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5663 (tm-30) REVERT: A 572 TYR cc_start: 0.6178 (t80) cc_final: 0.5765 (t80) REVERT: B 76 ASP cc_start: 0.7630 (t0) cc_final: 0.6898 (t0) REVERT: C 78 GLN cc_start: 0.7740 (mt0) cc_final: 0.7485 (mt0) outliers start: 9 outliers final: 4 residues processed: 151 average time/residue: 0.2151 time to fit residues: 41.1021 Evaluate side-chains 101 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.0030 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 overall best weight: 0.2866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 316 ASN A 332 GLN A 355 ASN A 368 ASN B 54 ASN B 101 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5122 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6394 Z= 0.151 Angle : 0.535 9.767 8665 Z= 0.277 Chirality : 0.040 0.256 948 Planarity : 0.005 0.030 1049 Dihedral : 9.425 76.936 1018 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.52 % Allowed : 15.73 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.30), residues: 759 helix: -0.10 (0.26), residues: 352 sheet: -1.22 (0.51), residues: 95 loop : -2.33 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 326 HIS 0.002 0.001 HIS A 143 PHE 0.027 0.001 PHE A 407 TYR 0.016 0.001 TYR A 358 ARG 0.004 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.657 Fit side-chains REVERT: A 279 LYS cc_start: 0.4017 (tptt) cc_final: 0.3398 (ttpp) REVERT: A 370 MET cc_start: 0.6237 (mmp) cc_final: 0.4073 (ttm) REVERT: A 389 MET cc_start: 0.4507 (mmt) cc_final: 0.4144 (mpp) REVERT: A 391 ASN cc_start: 0.7416 (t0) cc_final: 0.7162 (t0) REVERT: A 508 GLU cc_start: 0.6173 (tm-30) cc_final: 0.5737 (tm-30) REVERT: A 572 TYR cc_start: 0.6254 (t80) cc_final: 0.5901 (t80) REVERT: C 78 GLN cc_start: 0.7611 (mt0) cc_final: 0.7334 (mt0) REVERT: C 114 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.5599 (pp30) outliers start: 29 outliers final: 12 residues processed: 119 average time/residue: 0.1789 time to fit residues: 28.2379 Evaluate side-chains 107 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5230 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6394 Z= 0.219 Angle : 0.539 9.495 8665 Z= 0.280 Chirality : 0.040 0.241 948 Planarity : 0.004 0.030 1049 Dihedral : 8.696 71.653 1016 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.05 % Allowed : 18.69 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.30), residues: 759 helix: -0.24 (0.26), residues: 357 sheet: -1.06 (0.51), residues: 96 loop : -2.35 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.002 0.001 HIS C 100 PHE 0.028 0.001 PHE A 407 TYR 0.011 0.001 TYR A 358 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 267 TYR cc_start: 0.5381 (t80) cc_final: 0.5173 (t80) REVERT: A 279 LYS cc_start: 0.4110 (tptt) cc_final: 0.3420 (ttpp) REVERT: A 317 TRP cc_start: 0.6780 (m100) cc_final: 0.6404 (m100) REVERT: A 391 ASN cc_start: 0.7466 (t0) cc_final: 0.6831 (m-40) REVERT: A 508 GLU cc_start: 0.6244 (tm-30) cc_final: 0.5869 (tm-30) REVERT: A 572 TYR cc_start: 0.6141 (t80) cc_final: 0.5864 (t80) REVERT: C 78 GLN cc_start: 0.7630 (mt0) cc_final: 0.7244 (mt0) outliers start: 26 outliers final: 13 residues processed: 119 average time/residue: 0.1679 time to fit residues: 27.0030 Evaluate side-chains 109 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5314 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6394 Z= 0.249 Angle : 0.576 9.940 8665 Z= 0.301 Chirality : 0.041 0.205 948 Planarity : 0.005 0.033 1049 Dihedral : 7.650 59.926 1016 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.45 % Allowed : 18.54 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.29), residues: 759 helix: -0.29 (0.26), residues: 353 sheet: -1.12 (0.51), residues: 101 loop : -2.24 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 151 HIS 0.004 0.001 HIS A 456 PHE 0.021 0.002 PHE A 407 TYR 0.019 0.001 TYR A 142 ARG 0.003 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 267 TYR cc_start: 0.5736 (t80) cc_final: 0.5448 (t80) REVERT: A 279 LYS cc_start: 0.4037 (tptt) cc_final: 0.3494 (mtmm) REVERT: A 317 TRP cc_start: 0.6836 (m100) cc_final: 0.6495 (m100) REVERT: A 341 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.4636 (t80) REVERT: A 391 ASN cc_start: 0.7521 (t0) cc_final: 0.6858 (m-40) REVERT: A 422 PHE cc_start: 0.6772 (t80) cc_final: 0.6534 (t80) REVERT: A 508 GLU cc_start: 0.6161 (tm-30) cc_final: 0.5765 (tm-30) REVERT: A 562 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7288 (mm-40) REVERT: C 78 GLN cc_start: 0.7394 (mt0) cc_final: 0.6994 (mt0) outliers start: 35 outliers final: 23 residues processed: 127 average time/residue: 0.1705 time to fit residues: 29.2008 Evaluate side-chains 123 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.0040 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6394 Z= 0.219 Angle : 0.551 9.633 8665 Z= 0.288 Chirality : 0.040 0.203 948 Planarity : 0.004 0.037 1049 Dihedral : 6.614 58.407 1016 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.36 % Allowed : 21.03 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.29), residues: 759 helix: -0.38 (0.25), residues: 360 sheet: -0.79 (0.52), residues: 101 loop : -2.29 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 PHE 0.017 0.001 PHE A 407 TYR 0.023 0.001 TYR A 121 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 220 TRP cc_start: 0.5263 (m-90) cc_final: 0.4854 (m-90) REVERT: A 267 TYR cc_start: 0.5759 (t80) cc_final: 0.5511 (t80) REVERT: A 317 TRP cc_start: 0.6880 (m100) cc_final: 0.6564 (m100) REVERT: A 508 GLU cc_start: 0.6267 (tm-30) cc_final: 0.5880 (tm-30) REVERT: A 514 TRP cc_start: 0.6018 (m100) cc_final: 0.5655 (m-10) REVERT: A 562 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7278 (mm-40) REVERT: C 78 GLN cc_start: 0.7213 (mt0) cc_final: 0.6839 (mt0) outliers start: 28 outliers final: 23 residues processed: 119 average time/residue: 0.1467 time to fit residues: 24.6076 Evaluate side-chains 122 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 6394 Z= 0.407 Angle : 0.689 10.968 8665 Z= 0.366 Chirality : 0.046 0.263 948 Planarity : 0.005 0.034 1049 Dihedral : 6.795 57.366 1016 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 7.17 % Allowed : 19.16 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.28), residues: 759 helix: -0.81 (0.25), residues: 356 sheet: -1.05 (0.51), residues: 101 loop : -2.45 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 103 HIS 0.005 0.001 HIS A 235 PHE 0.020 0.002 PHE A 407 TYR 0.024 0.002 TYR A 121 ARG 0.003 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 220 TRP cc_start: 0.5226 (m-90) cc_final: 0.4574 (m-90) REVERT: A 328 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7662 (t0) REVERT: A 341 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.5466 (t80) REVERT: A 391 ASN cc_start: 0.7444 (t0) cc_final: 0.6954 (p0) REVERT: A 508 GLU cc_start: 0.6452 (tm-30) cc_final: 0.6194 (tm-30) REVERT: A 514 TRP cc_start: 0.6054 (m100) cc_final: 0.5625 (m-10) REVERT: A 562 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7442 (mm-40) REVERT: B 79 TYR cc_start: 0.7497 (m-80) cc_final: 0.6938 (m-80) outliers start: 46 outliers final: 31 residues processed: 137 average time/residue: 0.1564 time to fit residues: 29.3632 Evaluate side-chains 137 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.0060 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN C 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6394 Z= 0.194 Angle : 0.568 10.493 8665 Z= 0.299 Chirality : 0.041 0.220 948 Planarity : 0.004 0.040 1049 Dihedral : 5.914 54.509 1015 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.83 % Allowed : 22.59 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.29), residues: 759 helix: -0.56 (0.25), residues: 356 sheet: -0.87 (0.52), residues: 101 loop : -2.28 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 151 HIS 0.002 0.001 HIS A 143 PHE 0.020 0.001 PHE A 407 TYR 0.023 0.001 TYR A 121 ARG 0.002 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ASN cc_start: 0.3469 (t0) cc_final: 0.3118 (t0) REVERT: A 220 TRP cc_start: 0.5214 (m-90) cc_final: 0.4690 (m-90) REVERT: A 341 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.5244 (t80) REVERT: A 391 ASN cc_start: 0.7518 (t0) cc_final: 0.6991 (p0) REVERT: A 508 GLU cc_start: 0.6277 (tm-30) cc_final: 0.6054 (tm-30) REVERT: A 514 TRP cc_start: 0.6009 (m100) cc_final: 0.5548 (m-10) REVERT: A 537 TRP cc_start: 0.5203 (m100) cc_final: 0.4964 (m100) REVERT: A 562 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7371 (mm-40) REVERT: C 114 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6304 (pp30) outliers start: 31 outliers final: 21 residues processed: 128 average time/residue: 0.1569 time to fit residues: 27.5482 Evaluate side-chains 125 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 45 optimal weight: 0.0470 chunk 49 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 65 optimal weight: 0.0670 chunk 69 optimal weight: 0.0870 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6394 Z= 0.148 Angle : 0.543 10.345 8665 Z= 0.285 Chirality : 0.040 0.208 948 Planarity : 0.004 0.037 1049 Dihedral : 5.449 55.040 1015 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.58 % Allowed : 23.99 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.30), residues: 759 helix: -0.38 (0.26), residues: 358 sheet: -0.65 (0.53), residues: 101 loop : -2.11 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 204 HIS 0.001 0.001 HIS A 456 PHE 0.019 0.001 PHE A 454 TYR 0.013 0.001 TYR A 121 ARG 0.002 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.6608 (p) cc_final: 0.6388 (m) REVERT: A 220 TRP cc_start: 0.5263 (m-90) cc_final: 0.4859 (m-90) REVERT: A 301 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7500 (p) REVERT: A 341 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.5126 (t80) REVERT: A 385 TYR cc_start: 0.6364 (t80) cc_final: 0.6155 (t80) REVERT: A 514 TRP cc_start: 0.6024 (m100) cc_final: 0.5540 (m-10) REVERT: B 29 GLU cc_start: 0.8057 (mp0) cc_final: 0.7804 (mp0) REVERT: C 114 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6177 (pp30) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 0.1862 time to fit residues: 30.4596 Evaluate side-chains 107 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.0370 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6394 Z= 0.197 Angle : 0.561 10.253 8665 Z= 0.293 Chirality : 0.040 0.230 948 Planarity : 0.004 0.036 1049 Dihedral : 5.441 52.674 1015 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.96 % Allowed : 24.14 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.30), residues: 759 helix: -0.30 (0.26), residues: 357 sheet: -0.62 (0.54), residues: 101 loop : -1.99 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 317 HIS 0.002 0.001 HIS A 143 PHE 0.014 0.001 PHE A 604 TYR 0.030 0.001 TYR A 495 ARG 0.002 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.6603 (p) cc_final: 0.6375 (m) REVERT: A 220 TRP cc_start: 0.5267 (m-90) cc_final: 0.4794 (m-90) REVERT: A 279 LYS cc_start: 0.3749 (tptt) cc_final: 0.3218 (mtmm) REVERT: A 301 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7561 (p) REVERT: A 391 ASN cc_start: 0.7512 (t0) cc_final: 0.6992 (p0) REVERT: A 514 TRP cc_start: 0.6038 (m100) cc_final: 0.5561 (m-10) REVERT: C 114 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6162 (pp30) outliers start: 19 outliers final: 17 residues processed: 116 average time/residue: 0.1613 time to fit residues: 25.5221 Evaluate side-chains 119 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.989 > 50: distance: 43 - 47: 28.180 distance: 47 - 48: 48.827 distance: 47 - 184: 25.621 distance: 48 - 49: 30.983 distance: 48 - 51: 23.617 distance: 49 - 50: 8.274 distance: 49 - 58: 6.506 distance: 50 - 181: 28.305 distance: 51 - 52: 19.813 distance: 52 - 53: 24.453 distance: 52 - 54: 23.430 distance: 53 - 55: 24.252 distance: 54 - 56: 7.969 distance: 55 - 57: 22.024 distance: 56 - 57: 30.699 distance: 58 - 59: 8.133 distance: 59 - 60: 36.718 distance: 59 - 62: 14.096 distance: 60 - 61: 7.501 distance: 60 - 67: 28.018 distance: 62 - 63: 6.314 distance: 63 - 64: 16.537 distance: 64 - 65: 12.715 distance: 64 - 66: 7.991 distance: 67 - 68: 5.050 distance: 67 - 168: 28.333 distance: 68 - 69: 43.718 distance: 68 - 71: 4.520 distance: 69 - 70: 42.133 distance: 69 - 76: 14.217 distance: 70 - 165: 32.840 distance: 71 - 72: 19.936 distance: 72 - 73: 20.198 distance: 73 - 74: 16.562 distance: 73 - 75: 27.279 distance: 76 - 77: 18.177 distance: 77 - 78: 23.171 distance: 77 - 80: 29.484 distance: 78 - 79: 20.243 distance: 78 - 85: 20.909 distance: 80 - 81: 44.774 distance: 81 - 82: 33.418 distance: 82 - 83: 38.339 distance: 83 - 84: 27.176 distance: 85 - 86: 39.301 distance: 85 - 91: 10.752 distance: 86 - 87: 12.000 distance: 86 - 89: 18.765 distance: 87 - 88: 21.260 distance: 87 - 92: 31.294 distance: 89 - 90: 19.412 distance: 90 - 91: 40.127 distance: 92 - 93: 8.904 distance: 93 - 94: 30.189 distance: 94 - 95: 31.489 distance: 94 - 96: 21.078 distance: 96 - 97: 28.121 distance: 97 - 98: 16.231 distance: 97 - 100: 19.609 distance: 98 - 105: 43.871 distance: 100 - 101: 22.686 distance: 101 - 102: 30.612 distance: 102 - 103: 10.645 distance: 102 - 104: 52.927 distance: 105 - 106: 15.893 distance: 105 - 111: 25.751 distance: 106 - 107: 43.888 distance: 106 - 109: 15.863 distance: 107 - 108: 27.349 distance: 107 - 112: 25.615 distance: 109 - 110: 57.610 distance: 110 - 111: 12.210 distance: 112 - 113: 21.614 distance: 112 - 118: 11.554 distance: 113 - 114: 13.787 distance: 113 - 116: 35.051 distance: 114 - 115: 11.695 distance: 114 - 119: 48.912 distance: 116 - 117: 32.382 distance: 117 - 118: 30.622 distance: 119 - 120: 11.754 distance: 120 - 121: 8.081 distance: 120 - 123: 22.743 distance: 121 - 122: 10.316 distance: 121 - 128: 26.134 distance: 123 - 124: 6.654 distance: 124 - 125: 5.524 distance: 125 - 126: 21.386 distance: 126 - 127: 17.153