Starting phenix.real_space_refine on Mon Apr 8 16:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txt_26160/04_2024/7txt_26160_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txt_26160/04_2024/7txt_26160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txt_26160/04_2024/7txt_26160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txt_26160/04_2024/7txt_26160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txt_26160/04_2024/7txt_26160_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txt_26160/04_2024/7txt_26160_trim_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1855 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 35 5.16 5 C 4011 2.51 5 N 967 2.21 5 O 1079 1.98 5 F 1 1.80 5 H 6018 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 109": "OD1" <-> "OD2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 87": "OD1" <-> "OD2" Residue "S TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 247": "OD1" <-> "OD2" Residue "S GLU 396": "OE1" <-> "OE2" Residue "S PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 452": "OD1" <-> "OD2" Residue "S GLU 453": "OE1" <-> "OE2" Residue "S GLU 606": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12111 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1824 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1651 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "S" Number of atoms: 8636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8636 Unusual residues: {'KWC': 1} Inner-chain residues flagged as termini: ['pdbres="PRO S 617 "'] Classifications: {'peptide': 541, 'undetermined': 1} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 517, None: 1} Not linked: pdbres="PRO S 617 " pdbres="KWC S 701 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.82, per 1000 atoms: 0.48 Number of scatterers: 12111 At special positions: 0 Unit cell: (79.38, 72.09, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 F 1 9.00 O 1079 8.00 N 967 7.00 C 4011 6.00 H 6018 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 115 " distance=2.03 Simple disulfide: pdb=" SG CYS S 200 " - pdb=" SG CYS S 209 " 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=0, symmetry=0 Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 4 sheets defined 50.8% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'S' and resid 85 through 96 Processing helix chain 'S' and resid 99 through 111 removed outlier: 3.698A pdb=" N TRP S 103 " --> pdb=" O GLY S 100 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG S 104 " --> pdb=" O ASN S 101 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE S 105 " --> pdb=" O VAL S 102 " (cutoff:3.500A) Proline residue: S 106 - end of helix Processing helix chain 'S' and resid 114 through 126 Proline residue: S 120 - end of helix removed outlier: 3.745A pdb=" N MET S 124 " --> pdb=" O TYR S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 129 through 143 Processing helix chain 'S' and resid 149 through 152 Processing helix chain 'S' and resid 156 through 191 removed outlier: 4.126A pdb=" N GLY S 160 " --> pdb=" O ILE S 157 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR S 176 " --> pdb=" O ALA S 173 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASN S 177 " --> pdb=" O SER S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 234 Processing helix chain 'S' and resid 239 through 241 No H-bonds generated for 'chain 'S' and resid 239 through 241' Processing helix chain 'S' and resid 253 through 269 Processing helix chain 'S' and resid 274 through 284 removed outlier: 4.632A pdb=" N LYS S 279 " --> pdb=" O LYS S 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP S 282 " --> pdb=" O GLY S 278 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL S 283 " --> pdb=" O LYS S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 300 Processing helix chain 'S' and resid 305 through 313 Processing helix chain 'S' and resid 317 through 321 Processing helix chain 'S' and resid 323 through 337 Processing helix chain 'S' and resid 343 through 350 removed outlier: 3.777A pdb=" N TYR S 350 " --> pdb=" O ALA S 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 388 removed outlier: 3.615A pdb=" N VAL S 382 " --> pdb=" O VAL S 378 " (cutoff:3.500A) Processing helix chain 'S' and resid 394 through 398 Processing helix chain 'S' and resid 409 through 416 Processing helix chain 'S' and resid 420 through 453 removed outlier: 3.804A pdb=" N SER S 438 " --> pdb=" O LEU S 434 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL S 446 " --> pdb=" O GLY S 442 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 458 No H-bonds generated for 'chain 'S' and resid 455 through 458' Processing helix chain 'S' and resid 462 through 477 Processing helix chain 'S' and resid 479 through 481 No H-bonds generated for 'chain 'S' and resid 479 through 481' Processing helix chain 'S' and resid 485 through 495 Processing helix chain 'S' and resid 499 through 513 Processing helix chain 'S' and resid 518 through 529 Processing helix chain 'S' and resid 535 through 557 removed outlier: 4.922A pdb=" N SER S 545 " --> pdb=" O TRP S 541 " (cutoff:3.500A) Proline residue: S 546 - end of helix Processing helix chain 'S' and resid 572 through 599 removed outlier: 4.384A pdb=" N CYS S 588 " --> pdb=" O SER S 584 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE S 589 " --> pdb=" O SER S 585 " (cutoff:3.500A) Proline residue: S 590 - end of helix Processing helix chain 'S' and resid 604 through 612 removed outlier: 4.192A pdb=" N SER S 611 " --> pdb=" O ARG S 607 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 29 through 31 removed outlier: 5.537A pdb=" N LYS C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP C 66 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 37 through 42 Processing sheet with id= C, first strand: chain 'D' and resid 24 through 27 removed outlier: 3.577A pdb=" N TYR D 94 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 30 through 33 removed outlier: 5.937A pdb=" N LYS D 127 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL D 33 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU D 129 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN D 61 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU D 70 " --> pdb=" O GLN D 61 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 768 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: 4.87 Time building geometry restraints manager: 10.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5999 1.03 - 1.23: 32 1.23 - 1.42: 2745 1.42 - 1.62: 3468 1.62 - 1.81: 49 Bond restraints: 12293 Sorted by residual: bond pdb=" CAI KWC S 701 " pdb=" SAH KWC S 701 " ideal model delta sigma weight residual 1.750 1.458 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" CAB KWC S 701 " pdb=" FAA KWC S 701 " ideal model delta sigma weight residual 1.342 1.096 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" CAE KWC S 701 " pdb=" CAF KWC S 701 " ideal model delta sigma weight residual 1.470 1.308 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" CAG KWC S 701 " pdb=" SAH KWC S 701 " ideal model delta sigma weight residual 1.725 1.573 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CAK KWC S 701 " pdb=" CAL KWC S 701 " ideal model delta sigma weight residual 1.524 1.473 0.051 2.00e-02 2.50e+03 6.57e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 79.47 - 90.39: 4 90.39 - 101.30: 11 101.30 - 112.21: 13764 112.21 - 123.13: 7176 123.13 - 134.04: 1172 Bond angle restraints: 22127 Sorted by residual: angle pdb=" HB2 ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB3 ALA S 401 " ideal model delta sigma weight residual 110.00 79.47 30.53 3.00e+00 1.11e-01 1.04e+02 angle pdb=" HB1 ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB2 ALA S 401 " ideal model delta sigma weight residual 110.00 80.41 29.59 3.00e+00 1.11e-01 9.73e+01 angle pdb=" CA ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB3 ALA S 401 " ideal model delta sigma weight residual 109.00 79.72 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CA ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB1 ALA S 401 " ideal model delta sigma weight residual 109.00 81.70 27.30 3.00e+00 1.11e-01 8.28e+01 angle pdb=" CA ALA S 401 " pdb=" CB ALA S 401 " pdb=" HB2 ALA S 401 " ideal model delta sigma weight residual 109.00 131.86 -22.86 3.00e+00 1.11e-01 5.81e+01 ... (remaining 22122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5355 17.77 - 35.54: 327 35.54 - 53.30: 127 53.30 - 71.07: 36 71.07 - 88.84: 9 Dihedral angle restraints: 5854 sinusoidal: 3033 harmonic: 2821 Sorted by residual: dihedral pdb=" CB CYS C 41 " pdb=" SG CYS C 41 " pdb=" SG CYS C 115 " pdb=" CB CYS C 115 " ideal model delta sinusoidal sigma weight residual 93.00 59.30 33.70 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CA GLY S 402 " pdb=" C GLY S 402 " pdb=" N PRO S 403 " pdb=" CA PRO S 403 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ALA S 459 " pdb=" C ALA S 459 " pdb=" N LYS S 460 " pdb=" CA LYS S 460 " ideal model delta harmonic sigma weight residual 180.00 164.38 15.62 0 5.00e+00 4.00e-02 9.76e+00 ... (remaining 5851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 687 0.037 - 0.074: 188 0.074 - 0.112: 52 0.112 - 0.149: 10 0.149 - 0.186: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA ILE D 72 " pdb=" N ILE D 72 " pdb=" C ILE D 72 " pdb=" CB ILE D 72 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CA ILE D 41 " pdb=" N ILE D 41 " pdb=" C ILE D 41 " pdb=" CB ILE D 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE D 99 " pdb=" N ILE D 99 " pdb=" C ILE D 99 " pdb=" CB ILE D 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 935 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 271 " 0.015 2.00e-02 2.50e+03 1.01e-02 4.06e+00 pdb=" CG TRP S 271 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP S 271 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP S 271 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP S 271 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP S 271 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 271 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 271 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 271 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP S 271 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP S 271 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP S 271 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP S 271 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP S 271 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP S 271 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP S 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE S 130 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO S 131 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO S 131 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 131 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS S 155 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO S 156 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO S 156 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 156 " 0.022 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 562 2.16 - 2.77: 23873 2.77 - 3.38: 37076 3.38 - 3.99: 48203 3.99 - 4.60: 76039 Nonbonded interactions: 185753 Sorted by model distance: nonbonded pdb=" HE ARG C 38 " pdb=" OE1 GLN C 101 " model vdw 1.544 1.850 nonbonded pdb=" O ILE S 544 " pdb=" H PHE S 548 " model vdw 1.588 1.850 nonbonded pdb=" O THR S 603 " pdb=" H ARG S 607 " model vdw 1.594 1.850 nonbonded pdb=" O LEU S 492 " pdb=" H ALA S 496 " model vdw 1.614 1.850 nonbonded pdb=" OE2 GLU S 444 " pdb=" HG1 THR S 448 " model vdw 1.637 1.850 ... (remaining 185748 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 individual isotropic 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.190 Extract box with map and model: 10.240 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 45.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.007 0.292 6275 Z= 0.403 Angle : 0.530 11.580 8543 Z= 0.285 Chirality : 0.039 0.186 938 Planarity : 0.004 0.047 1053 Dihedral : 12.667 88.841 2166 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 766 helix: 0.70 (0.26), residues: 387 sheet: -0.54 (0.45), residues: 125 loop : -0.05 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP S 271 HIS 0.003 0.001 HIS S 143 PHE 0.016 0.001 PHE S 548 TYR 0.017 0.001 TYR D 73 ARG 0.007 0.000 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.913 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 2.7077 time to fit residues: 348.5843 Evaluate side-chains 97 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN S 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6275 Z= 0.232 Angle : 0.502 5.137 8543 Z= 0.268 Chirality : 0.038 0.163 938 Planarity : 0.004 0.047 1053 Dihedral : 4.137 20.870 849 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.39 % Allowed : 8.82 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.31), residues: 766 helix: 0.68 (0.26), residues: 387 sheet: -0.48 (0.46), residues: 125 loop : 0.02 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.005 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: D 104 GLU cc_start: 0.7252 (tp30) cc_final: 0.6952 (tp30) REVERT: S 311 PHE cc_start: 0.7877 (m-10) cc_final: 0.7537 (m-10) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 2.3568 time to fit residues: 246.2921 Evaluate side-chains 101 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 327 ILE Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.0170 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6275 Z= 0.220 Angle : 0.489 5.112 8543 Z= 0.260 Chirality : 0.038 0.154 938 Planarity : 0.004 0.055 1053 Dihedral : 3.943 14.338 849 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.77 % Allowed : 8.98 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.31), residues: 766 helix: 0.64 (0.27), residues: 388 sheet: -0.33 (0.46), residues: 122 loop : 0.06 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.023 0.001 TYR D 73 ARG 0.005 0.000 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: D 104 GLU cc_start: 0.7239 (tp30) cc_final: 0.6962 (tp30) outliers start: 5 outliers final: 4 residues processed: 100 average time/residue: 2.4633 time to fit residues: 259.6396 Evaluate side-chains 101 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN S 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6275 Z= 0.279 Angle : 0.500 5.092 8543 Z= 0.268 Chirality : 0.039 0.150 938 Planarity : 0.004 0.058 1053 Dihedral : 3.913 14.501 849 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.08 % Allowed : 9.44 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 766 helix: 0.59 (0.26), residues: 388 sheet: -0.35 (0.46), residues: 122 loop : 0.03 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.018 0.001 PHE S 548 TYR 0.024 0.001 TYR D 73 ARG 0.005 0.000 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: C 47 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7527 (ptm-80) REVERT: C 123 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7409 (mp0) outliers start: 7 outliers final: 4 residues processed: 100 average time/residue: 2.5318 time to fit residues: 266.3369 Evaluate side-chains 100 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 223 HIS S 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6275 Z= 0.272 Angle : 0.498 5.061 8543 Z= 0.266 Chirality : 0.038 0.152 938 Planarity : 0.004 0.062 1053 Dihedral : 3.910 14.576 849 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.08 % Allowed : 10.22 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.31), residues: 766 helix: 0.61 (0.26), residues: 387 sheet: -0.35 (0.45), residues: 122 loop : 0.01 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.023 0.001 TYR D 73 ARG 0.005 0.000 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.034 Fit side-chains REVERT: C 47 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7559 (ptm-80) REVERT: C 123 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: D 104 GLU cc_start: 0.7397 (tp30) cc_final: 0.6980 (tp30) outliers start: 7 outliers final: 4 residues processed: 99 average time/residue: 2.5480 time to fit residues: 265.3655 Evaluate side-chains 102 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 193 ASP Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6275 Z= 0.209 Angle : 0.488 5.026 8543 Z= 0.259 Chirality : 0.038 0.154 938 Planarity : 0.004 0.064 1053 Dihedral : 3.842 15.081 849 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.24 % Allowed : 10.37 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.31), residues: 766 helix: 0.64 (0.26), residues: 387 sheet: -0.32 (0.45), residues: 122 loop : 0.04 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.023 0.001 TYR D 73 ARG 0.007 0.000 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.129 Fit side-chains REVERT: C 47 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7547 (ptm-80) REVERT: C 123 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: D 104 GLU cc_start: 0.7346 (tp30) cc_final: 0.7007 (tp30) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 2.5980 time to fit residues: 270.5106 Evaluate side-chains 100 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6275 Z= 0.240 Angle : 0.489 5.176 8543 Z= 0.260 Chirality : 0.038 0.153 938 Planarity : 0.004 0.071 1053 Dihedral : 3.864 14.796 849 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.24 % Allowed : 10.53 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.31), residues: 766 helix: 0.67 (0.26), residues: 387 sheet: -0.35 (0.45), residues: 122 loop : -0.00 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.021 0.001 TYR D 73 ARG 0.009 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.014 Fit side-chains REVERT: C 47 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7558 (ptm-80) REVERT: C 123 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7414 (mp0) outliers start: 8 outliers final: 5 residues processed: 93 average time/residue: 2.4549 time to fit residues: 240.9023 Evaluate side-chains 96 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6275 Z= 0.232 Angle : 0.497 5.442 8543 Z= 0.263 Chirality : 0.038 0.153 938 Planarity : 0.004 0.074 1053 Dihedral : 3.850 15.096 849 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.08 % Allowed : 10.84 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.31), residues: 766 helix: 0.70 (0.26), residues: 387 sheet: -0.34 (0.45), residues: 122 loop : 0.03 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.009 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.962 Fit side-chains REVERT: C 47 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7526 (ptm-80) REVERT: C 123 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7405 (mp0) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 2.4742 time to fit residues: 245.3842 Evaluate side-chains 96 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6275 Z= 0.210 Angle : 0.486 5.619 8543 Z= 0.257 Chirality : 0.038 0.154 938 Planarity : 0.004 0.074 1053 Dihedral : 3.825 14.620 849 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.93 % Allowed : 11.15 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.31), residues: 766 helix: 0.74 (0.27), residues: 387 sheet: -0.34 (0.45), residues: 122 loop : 0.07 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 103 HIS 0.002 0.001 HIS S 143 PHE 0.017 0.001 PHE S 548 TYR 0.022 0.001 TYR D 73 ARG 0.012 0.001 ARG S 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.025 Fit side-chains REVERT: C 47 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7495 (ptm-80) REVERT: C 123 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7413 (mp0) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 2.3844 time to fit residues: 246.5591 Evaluate side-chains 97 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6275 Z= 0.268 Angle : 0.511 5.534 8543 Z= 0.271 Chirality : 0.038 0.155 938 Planarity : 0.004 0.078 1053 Dihedral : 3.846 14.612 849 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.08 % Allowed : 11.15 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.31), residues: 766 helix: 0.73 (0.26), residues: 388 sheet: -0.36 (0.45), residues: 122 loop : 0.03 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 103 HIS 0.003 0.001 HIS S 143 PHE 0.018 0.001 PHE S 548 TYR 0.021 0.001 TYR D 73 ARG 0.011 0.001 ARG S 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 201 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.933 Fit side-chains REVERT: C 47 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7480 (ptm-80) REVERT: C 123 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7415 (mp0) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 2.4138 time to fit residues: 249.3462 Evaluate side-chains 101 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain S residue 493 GLU Chi-restraints excluded: chain S residue 612 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.085423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.073695 restraints weight = 31332.063| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.09 r_work: 0.2727 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6275 Z= 0.182 Angle : 0.492 5.561 8543 Z= 0.259 Chirality : 0.038 0.156 938 Planarity : 0.004 0.076 1053 Dihedral : 3.791 14.685 849 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.08 % Allowed : 11.30 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.31), residues: 766 helix: 0.79 (0.27), residues: 387 sheet: -0.32 (0.45), residues: 122 loop : 0.09 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 103 HIS 0.002 0.001 HIS S 143 PHE 0.016 0.001 PHE S 548 TYR 0.023 0.001 TYR D 73 ARG 0.012 0.001 ARG S 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5636.19 seconds wall clock time: 100 minutes 17.27 seconds (6017.27 seconds total)