Starting phenix.real_space_refine on Fri Nov 15 00:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/11_2024/8fy4_29552.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/11_2024/8fy4_29552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/11_2024/8fy4_29552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/11_2024/8fy4_29552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/11_2024/8fy4_29552.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/11_2024/8fy4_29552.cif" } resolution = 2.57 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5016 2.51 5 N 1332 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7800 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1803 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 4326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4326 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 532} Chain breaks: 7 Chain: "C" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.29, per 1000 atoms: 0.68 Number of scatterers: 7800 At special positions: 0 Unit cell: (70.854, 80.976, 151.107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1412 8.00 N 1332 7.00 C 5016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 74.3% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 54 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 67 through 82 removed outlier: 4.191A pdb=" N ILE A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.687A pdb=" N ASN A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.960A pdb=" N VAL A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 162 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.670A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.282A pdb=" N LEU A 240 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 40 removed outlier: 3.883A pdb=" N LEU B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 56 Processing helix chain 'B' and resid 59 through 74 removed outlier: 4.251A pdb=" N THR B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.509A pdb=" N TYR B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.949A pdb=" N PHE B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 163 through 180 Processing helix chain 'B' and resid 205 through 230 removed outlier: 3.606A pdb=" N ALA B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 4.375A pdb=" N ARG B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 265 through 276 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 308 through 329 removed outlier: 3.566A pdb=" N PHE B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.935A pdb=" N LYS B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.528A pdb=" N LEU B 350 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 388 through 403 Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.757A pdb=" N ILE B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 547 Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 566 through 584 Processing helix chain 'B' and resid 586 through 594 removed outlier: 3.776A pdb=" N THR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 637 through 656 Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.851A pdb=" N ILE B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 695 through 706 removed outlier: 3.786A pdb=" N GLN B 701 " --> pdb=" O GLN B 697 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.581A pdb=" N SER C 47 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 64 through 78 removed outlier: 3.753A pdb=" N VAL C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 removed outlier: 3.603A pdb=" N ARG C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 109 through 117 removed outlier: 3.986A pdb=" N PHE C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.693A pdb=" N PHE C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 4.032A pdb=" N ILE C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.847A pdb=" N GLU C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 224 through 233 Processing sheet with id=AA1, first strand: chain 'C' and resid 203 through 204 494 hydrogen bonds defined for protein. 1443 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: 2.09 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2516 1.34 - 1.46: 1455 1.46 - 1.58: 3929 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 7957 Sorted by residual: bond pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CG LYS C 31 " pdb=" CD LYS C 31 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB GLN B 137 " pdb=" CG GLN B 137 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB ASP A 237 " pdb=" CG ASP A 237 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB LYS C 31 " pdb=" CG LYS C 31 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 7952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 10657 2.59 - 5.18: 89 5.18 - 7.77: 9 7.77 - 10.36: 2 10.36 - 12.95: 2 Bond angle restraints: 10759 Sorted by residual: angle pdb=" CB MET C 170 " pdb=" CG MET C 170 " pdb=" SD MET C 170 " ideal model delta sigma weight residual 112.70 125.65 -12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CA LYS B 176 " pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " ideal model delta sigma weight residual 116.30 128.27 -11.97 3.50e+00 8.16e-02 1.17e+01 angle pdb=" CB LYS C 31 " pdb=" CG LYS C 31 " pdb=" CD LYS C 31 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " pdb=" CD LYS B 176 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.90e+00 ... (remaining 10754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4345 17.75 - 35.50: 391 35.50 - 53.26: 100 53.26 - 71.01: 21 71.01 - 88.76: 4 Dihedral angle restraints: 4861 sinusoidal: 1959 harmonic: 2902 Sorted by residual: dihedral pdb=" CA ASP C 209 " pdb=" CB ASP C 209 " pdb=" CG ASP C 209 " pdb=" OD1 ASP C 209 " ideal model delta sinusoidal sigma weight residual -30.00 -86.66 56.66 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP C 259 " pdb=" CB ASP C 259 " pdb=" CG ASP C 259 " pdb=" OD1 ASP C 259 " ideal model delta sinusoidal sigma weight residual -30.00 -85.21 55.21 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CB MET B 285 " pdb=" CG MET B 285 " pdb=" SD MET B 285 " pdb=" CE MET B 285 " ideal model delta sinusoidal sigma weight residual 180.00 120.92 59.08 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 809 0.027 - 0.054: 263 0.054 - 0.081: 101 0.081 - 0.108: 45 0.108 - 0.136: 13 Chirality restraints: 1231 Sorted by residual: chirality pdb=" CA ILE B 424 " pdb=" N ILE B 424 " pdb=" C ILE B 424 " pdb=" CB ILE B 424 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CB ILE C 181 " pdb=" CA ILE C 181 " pdb=" CG1 ILE C 181 " pdb=" CG2 ILE C 181 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 453 " pdb=" N ILE B 453 " pdb=" C ILE B 453 " pdb=" CB ILE B 453 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1228 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 141 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 142 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 64 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" CD GLU C 64 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU C 64 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 163 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO C 164 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.020 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 387 2.73 - 3.27: 8194 3.27 - 3.82: 13833 3.82 - 4.36: 15628 4.36 - 4.90: 27191 Nonbonded interactions: 65233 Sorted by model distance: nonbonded pdb=" N GLN C 226 " pdb=" OE1 GLN C 226 " model vdw 2.189 3.120 nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 163 " model vdw 2.206 3.040 nonbonded pdb=" O PHE A 214 " pdb=" OH TYR A 228 " model vdw 2.217 3.040 nonbonded pdb=" N GLN C 274 " pdb=" OE1 GLN C 274 " model vdw 2.218 3.120 nonbonded pdb=" N GLU A 179 " pdb=" OE1 GLU A 179 " model vdw 2.229 3.120 ... (remaining 65228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.350 Find NCS groups from input model: 0.080 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 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 0.043 7957 Z= 0.178 Angle : 0.570 12.948 10759 Z= 0.280 Chirality : 0.036 0.136 1231 Planarity : 0.004 0.043 1371 Dihedral : 14.867 88.761 2965 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.87 % Allowed : 18.55 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 2.42 (0.28), residues: 957 helix: 2.16 (0.21), residues: 681 sheet: None (None), residues: 0 loop : 0.27 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 275 HIS 0.003 0.001 HIS B 430 PHE 0.009 0.001 PHE B 284 TYR 0.017 0.001 TYR B 136 ARG 0.004 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.864 Fit side-chains REVERT: A 31 GLU cc_start: 0.6566 (tt0) cc_final: 0.6320 (tt0) REVERT: A 67 ASP cc_start: 0.7051 (p0) cc_final: 0.6842 (p0) REVERT: A 138 SER cc_start: 0.7279 (m) cc_final: 0.6682 (p) REVERT: B 243 MET cc_start: 0.0653 (mmt) cc_final: 0.0161 (mmt) REVERT: B 285 MET cc_start: 0.3848 (mmp) cc_final: 0.2687 (mmp) REVERT: B 459 GLU cc_start: 0.6679 (mp0) cc_final: 0.6115 (mp0) REVERT: B 530 ASN cc_start: 0.5968 (t0) cc_final: 0.5729 (t0) REVERT: B 548 ASP cc_start: 0.6645 (t0) cc_final: 0.6314 (t0) REVERT: B 549 ASN cc_start: 0.7057 (m-40) cc_final: 0.6553 (p0) REVERT: B 551 MET cc_start: 0.7028 (mmm) cc_final: 0.6682 (mmp) REVERT: B 561 GLN cc_start: 0.7167 (mt0) cc_final: 0.6544 (mp10) REVERT: B 582 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6711 (mt) REVERT: B 664 LYS cc_start: 0.6414 (ttmm) cc_final: 0.6190 (ttmt) REVERT: C 182 SER cc_start: 0.6862 (t) cc_final: 0.6594 (m) REVERT: C 190 GLU cc_start: 0.6851 (tp30) cc_final: 0.6497 (tp30) outliers start: 16 outliers final: 8 residues processed: 138 average time/residue: 1.2415 time to fit residues: 181.7222 Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 102 GLN A 135 ASN A 151 GLN A 216 GLN B 88 GLN B 163 GLN B 169 HIS ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 364 GLN B 383 GLN B 549 ASN B 561 GLN B 632 GLN B 695 ASN C 58 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN C 192 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7957 Z= 0.273 Angle : 0.674 9.809 10759 Z= 0.339 Chirality : 0.041 0.159 1231 Planarity : 0.005 0.072 1371 Dihedral : 5.300 55.498 1060 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.02 % Allowed : 16.10 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 957 helix: 1.71 (0.20), residues: 685 sheet: None (None), residues: 0 loop : 0.05 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 263 HIS 0.009 0.002 HIS B 303 PHE 0.023 0.002 PHE B 295 TYR 0.018 0.002 TYR B 429 ARG 0.014 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 114 GLN cc_start: 0.6937 (mt0) cc_final: 0.6584 (mm110) REVERT: A 138 SER cc_start: 0.7206 (m) cc_final: 0.6834 (t) REVERT: B 176 LYS cc_start: 0.5970 (tmmt) cc_final: 0.5712 (tmmt) REVERT: B 265 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6537 (p0) REVERT: B 268 LYS cc_start: 0.6451 (tttp) cc_final: 0.5971 (ttpt) REVERT: B 285 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4650 (mmp) REVERT: B 317 LYS cc_start: 0.6158 (mtmp) cc_final: 0.5901 (mtmp) REVERT: B 459 GLU cc_start: 0.7087 (mp0) cc_final: 0.6420 (mp0) REVERT: B 530 ASN cc_start: 0.6232 (t0) cc_final: 0.5928 (t0) REVERT: B 561 GLN cc_start: 0.7301 (mt0) cc_final: 0.6707 (mp10) REVERT: B 582 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.7022 (mt) REVERT: B 656 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7474 (mtm180) REVERT: B 658 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6684 (mt-10) REVERT: B 698 LEU cc_start: 0.6547 (tt) cc_final: 0.6292 (tm) outliers start: 43 outliers final: 11 residues processed: 171 average time/residue: 1.2418 time to fit residues: 225.0376 Evaluate side-chains 137 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 200 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN B 693 ASN C 58 HIS C 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 7957 Z= 0.411 Angle : 0.702 9.158 10759 Z= 0.353 Chirality : 0.044 0.178 1231 Planarity : 0.005 0.048 1371 Dihedral : 5.008 41.655 1052 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.90 % Allowed : 18.90 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 957 helix: 1.20 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -0.20 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 296 HIS 0.007 0.001 HIS C 58 PHE 0.017 0.002 PHE B 254 TYR 0.022 0.002 TYR B 688 ARG 0.004 0.001 ARG B 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.871 Fit side-chains REVERT: A 76 GLN cc_start: 0.6829 (tt0) cc_final: 0.6264 (tt0) REVERT: A 77 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.5869 (mp0) REVERT: A 114 GLN cc_start: 0.6817 (mt0) cc_final: 0.6593 (mm-40) REVERT: A 184 LEU cc_start: 0.7168 (tt) cc_final: 0.6948 (tt) REVERT: A 216 GLN cc_start: 0.6972 (mt0) cc_final: 0.6680 (mt0) REVERT: B 123 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7166 (mtt180) REVERT: B 127 GLU cc_start: 0.6488 (mp0) cc_final: 0.6166 (mp0) REVERT: B 143 GLU cc_start: 0.5813 (tm-30) cc_final: 0.5478 (tm-30) REVERT: B 176 LYS cc_start: 0.6075 (tmmt) cc_final: 0.5807 (tmmt) REVERT: B 243 MET cc_start: 0.2138 (mmt) cc_final: 0.1883 (mmt) REVERT: B 252 SER cc_start: 0.7067 (m) cc_final: 0.6757 (p) REVERT: B 267 ARG cc_start: 0.7043 (mmt180) cc_final: 0.6808 (mmt-90) REVERT: B 352 ASN cc_start: 0.7391 (t0) cc_final: 0.7097 (t0) REVERT: B 380 GLU cc_start: 0.6638 (tp30) cc_final: 0.6205 (mm-30) REVERT: B 397 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 561 GLN cc_start: 0.7339 (mt0) cc_final: 0.6691 (mp10) REVERT: B 569 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7018 (mp) REVERT: B 642 ARG cc_start: 0.6744 (mtt90) cc_final: 0.6428 (mtt-85) REVERT: B 690 GLU cc_start: 0.7630 (mm-30) cc_final: 0.6928 (mm-30) REVERT: C 64 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6672 (pp20) REVERT: C 68 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7724 (tp) REVERT: C 98 MET cc_start: 0.8082 (mtt) cc_final: 0.7637 (mtp) REVERT: C 150 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5835 (pp30) REVERT: C 229 GLU cc_start: 0.6987 (tt0) cc_final: 0.6760 (tt0) REVERT: C 245 PRO cc_start: 0.7925 (Cg_exo) cc_final: 0.7713 (Cg_endo) outliers start: 42 outliers final: 10 residues processed: 195 average time/residue: 1.3127 time to fit residues: 270.2741 Evaluate side-chains 162 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 150 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 81 ASN B 108 ASN B 265 ASN B 310 ASN B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 7957 Z= 0.333 Angle : 0.605 9.653 10759 Z= 0.300 Chirality : 0.040 0.159 1231 Planarity : 0.005 0.051 1371 Dihedral : 4.311 30.218 1046 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.50 % Allowed : 21.82 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 957 helix: 1.43 (0.19), residues: 693 sheet: None (None), residues: 0 loop : -0.06 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 275 HIS 0.006 0.001 HIS B 303 PHE 0.023 0.002 PHE C 247 TYR 0.014 0.002 TYR B 261 ARG 0.005 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.939 Fit side-chains REVERT: A 29 GLN cc_start: 0.7545 (tt0) cc_final: 0.7192 (tt0) REVERT: A 76 GLN cc_start: 0.6789 (tt0) cc_final: 0.6454 (tt0) REVERT: A 114 GLN cc_start: 0.6759 (mt0) cc_final: 0.6556 (mm-40) REVERT: A 216 GLN cc_start: 0.7001 (mt0) cc_final: 0.6762 (mt0) REVERT: B 123 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7178 (mtt-85) REVERT: B 127 GLU cc_start: 0.6551 (mp0) cc_final: 0.6166 (mp0) REVERT: B 176 LYS cc_start: 0.6286 (tmmt) cc_final: 0.5964 (tmmt) REVERT: B 267 ARG cc_start: 0.7104 (mmt180) cc_final: 0.6842 (mmt-90) REVERT: B 380 GLU cc_start: 0.6676 (tp30) cc_final: 0.6276 (mm-30) REVERT: B 397 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7202 (mt-10) REVERT: B 561 GLN cc_start: 0.7339 (mt0) cc_final: 0.6586 (mp10) REVERT: B 569 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7038 (mp) REVERT: B 658 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6715 (mt-10) REVERT: B 690 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7134 (mm-30) REVERT: C 64 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6761 (pp20) REVERT: C 98 MET cc_start: 0.8118 (mtt) cc_final: 0.7784 (mtp) REVERT: C 229 GLU cc_start: 0.7052 (tt0) cc_final: 0.6833 (tt0) outliers start: 30 outliers final: 12 residues processed: 174 average time/residue: 1.3970 time to fit residues: 256.0669 Evaluate side-chains 170 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.0050 chunk 0 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 125 GLN B 108 ASN B 148 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN B 549 ASN B 554 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.6945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7957 Z= 0.236 Angle : 0.555 8.422 10759 Z= 0.276 Chirality : 0.038 0.153 1231 Planarity : 0.005 0.044 1371 Dihedral : 4.130 27.398 1046 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.32 % Allowed : 22.05 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.27), residues: 957 helix: 1.58 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.04 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 275 HIS 0.006 0.001 HIS B 386 PHE 0.018 0.002 PHE C 247 TYR 0.013 0.001 TYR B 355 ARG 0.006 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.748 Fit side-chains REVERT: A 29 GLN cc_start: 0.7541 (tt0) cc_final: 0.7147 (mt0) REVERT: A 76 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: A 216 GLN cc_start: 0.7018 (mt0) cc_final: 0.6799 (mt0) REVERT: B 123 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7155 (mtt-85) REVERT: B 127 GLU cc_start: 0.6641 (mp0) cc_final: 0.6263 (mp0) REVERT: B 148 GLN cc_start: 0.6822 (mt0) cc_final: 0.6609 (mt0) REVERT: B 263 ARG cc_start: 0.6940 (mtp180) cc_final: 0.6664 (mtt180) REVERT: B 267 ARG cc_start: 0.7078 (mmt180) cc_final: 0.6836 (mmt-90) REVERT: B 349 LEU cc_start: 0.6042 (mt) cc_final: 0.5768 (mt) REVERT: B 380 GLU cc_start: 0.6681 (tp30) cc_final: 0.6290 (mm-30) REVERT: B 397 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7225 (mt-10) REVERT: B 561 GLN cc_start: 0.7359 (mt0) cc_final: 0.6602 (mp10) REVERT: B 569 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7052 (mp) REVERT: B 633 CYS cc_start: 0.7419 (m) cc_final: 0.7141 (p) REVERT: B 690 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7097 (mm-30) REVERT: C 64 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6702 (pp20) REVERT: C 68 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7642 (tp) REVERT: C 98 MET cc_start: 0.8106 (mtt) cc_final: 0.7774 (mtp) REVERT: C 151 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7080 (mp) REVERT: C 229 GLU cc_start: 0.7072 (tt0) cc_final: 0.6846 (tt0) outliers start: 37 outliers final: 16 residues processed: 180 average time/residue: 1.2765 time to fit residues: 242.4223 Evaluate side-chains 179 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 226 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 108 ASN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 549 ASN B 554 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7957 Z= 0.223 Angle : 0.548 8.779 10759 Z= 0.269 Chirality : 0.038 0.160 1231 Planarity : 0.004 0.043 1371 Dihedral : 4.046 27.172 1046 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.67 % Allowed : 22.05 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 957 helix: 1.65 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.01 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 275 HIS 0.004 0.001 HIS B 303 PHE 0.018 0.001 PHE C 247 TYR 0.014 0.001 TYR B 355 ARG 0.006 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7527 (tt0) cc_final: 0.7319 (mt0) REVERT: A 213 ASP cc_start: 0.6266 (m-30) cc_final: 0.5908 (m-30) REVERT: A 216 GLN cc_start: 0.7025 (mt0) cc_final: 0.6806 (mt0) REVERT: B 123 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7130 (mtt-85) REVERT: B 127 GLU cc_start: 0.6684 (mp0) cc_final: 0.6185 (mp0) REVERT: B 230 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6510 (mtpt) REVERT: B 263 ARG cc_start: 0.6920 (mtt180) cc_final: 0.6651 (mtt180) REVERT: B 267 ARG cc_start: 0.7074 (mmt180) cc_final: 0.6834 (mmt-90) REVERT: B 349 LEU cc_start: 0.6121 (mt) cc_final: 0.5848 (mt) REVERT: B 380 GLU cc_start: 0.6682 (tp30) cc_final: 0.6280 (mm-30) REVERT: B 387 SER cc_start: 0.7665 (t) cc_final: 0.7118 (m) REVERT: B 397 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 455 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7269 (p) REVERT: B 561 GLN cc_start: 0.7321 (mt0) cc_final: 0.6566 (mp10) REVERT: B 569 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7036 (mp) REVERT: B 633 CYS cc_start: 0.7376 (m) cc_final: 0.7096 (p) REVERT: B 690 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7078 (mm-30) REVERT: C 64 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6714 (pp20) REVERT: C 68 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7660 (tp) REVERT: C 98 MET cc_start: 0.8101 (mtt) cc_final: 0.7783 (mtp) REVERT: C 229 GLU cc_start: 0.7058 (tt0) cc_final: 0.6842 (tt0) outliers start: 40 outliers final: 15 residues processed: 172 average time/residue: 1.3542 time to fit residues: 245.1978 Evaluate side-chains 166 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 226 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 114 GLN B 108 ASN B 386 HIS B 449 GLN B 554 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.7567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7957 Z= 0.307 Angle : 0.595 9.942 10759 Z= 0.290 Chirality : 0.041 0.161 1231 Planarity : 0.005 0.044 1371 Dihedral : 4.177 28.513 1046 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.55 % Allowed : 21.35 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 957 helix: 1.52 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.08 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 296 HIS 0.005 0.001 HIS B 303 PHE 0.020 0.002 PHE C 243 TYR 0.014 0.002 TYR B 355 ARG 0.006 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 33 GLN cc_start: 0.7062 (tp-100) cc_final: 0.6687 (tt0) REVERT: A 213 ASP cc_start: 0.6301 (m-30) cc_final: 0.5944 (m-30) REVERT: B 123 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7205 (mtt-85) REVERT: B 127 GLU cc_start: 0.6744 (mp0) cc_final: 0.6274 (mp0) REVERT: B 267 ARG cc_start: 0.7084 (mmt180) cc_final: 0.6825 (mmt-90) REVERT: B 285 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6348 (mmt) REVERT: B 289 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6582 (mt-10) REVERT: B 380 GLU cc_start: 0.6717 (tp30) cc_final: 0.6333 (mm-30) REVERT: B 387 SER cc_start: 0.7670 (t) cc_final: 0.7183 (m) REVERT: B 397 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7217 (mt-10) REVERT: B 455 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 561 GLN cc_start: 0.7324 (mt0) cc_final: 0.6544 (mp10) REVERT: B 569 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7160 (mp) REVERT: B 633 CYS cc_start: 0.7378 (m) cc_final: 0.6943 (p) REVERT: B 690 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7150 (mm-30) REVERT: C 64 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6661 (pp20) REVERT: C 68 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7701 (tp) REVERT: C 98 MET cc_start: 0.8102 (mtt) cc_final: 0.7773 (mtp) REVERT: C 229 GLU cc_start: 0.7055 (tt0) cc_final: 0.6839 (tt0) REVERT: C 243 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7519 (p90) outliers start: 39 outliers final: 14 residues processed: 174 average time/residue: 1.3130 time to fit residues: 241.4424 Evaluate side-chains 173 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.0060 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 90 optimal weight: 0.6980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 388 ASN B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.7708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7957 Z= 0.230 Angle : 0.559 8.563 10759 Z= 0.273 Chirality : 0.039 0.147 1231 Planarity : 0.004 0.044 1371 Dihedral : 4.024 27.715 1046 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.20 % Allowed : 22.40 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 957 helix: 1.71 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.02 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 275 HIS 0.004 0.001 HIS B 303 PHE 0.018 0.002 PHE C 243 TYR 0.012 0.001 TYR B 355 ARG 0.006 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 213 ASP cc_start: 0.6251 (m-30) cc_final: 0.5900 (m-30) REVERT: B 123 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7230 (mtt-85) REVERT: B 127 GLU cc_start: 0.6726 (mp0) cc_final: 0.6277 (mp0) REVERT: B 263 ARG cc_start: 0.6936 (mtt180) cc_final: 0.6681 (mtt180) REVERT: B 267 ARG cc_start: 0.7077 (mmt180) cc_final: 0.6822 (mmt-90) REVERT: B 285 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6340 (mmt) REVERT: B 289 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6625 (mt-10) REVERT: B 380 GLU cc_start: 0.6733 (tp30) cc_final: 0.6366 (mm-30) REVERT: B 387 SER cc_start: 0.7595 (t) cc_final: 0.7137 (m) REVERT: B 397 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7233 (mt-10) REVERT: B 455 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7311 (p) REVERT: B 561 GLN cc_start: 0.7336 (mt0) cc_final: 0.6551 (mp10) REVERT: B 569 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6974 (mp) REVERT: B 633 CYS cc_start: 0.7350 (m) cc_final: 0.7104 (p) REVERT: B 690 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7090 (mm-30) REVERT: C 64 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6667 (pp20) REVERT: C 68 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7645 (tp) REVERT: C 98 MET cc_start: 0.8111 (mtt) cc_final: 0.7808 (mtp) REVERT: C 229 GLU cc_start: 0.7056 (tt0) cc_final: 0.6833 (tt0) REVERT: C 243 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7544 (p90) outliers start: 36 outliers final: 15 residues processed: 175 average time/residue: 1.3489 time to fit residues: 249.0058 Evaluate side-chains 173 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 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 216 GLN B 108 ASN B 549 ASN B 554 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7957 Z= 0.300 Angle : 0.601 10.509 10759 Z= 0.293 Chirality : 0.041 0.151 1231 Planarity : 0.005 0.044 1371 Dihedral : 4.129 28.377 1046 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.27 % Allowed : 23.22 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.27), residues: 957 helix: 1.60 (0.19), residues: 697 sheet: None (None), residues: 0 loop : -0.07 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.005 0.001 HIS B 303 PHE 0.020 0.002 PHE C 247 TYR 0.012 0.001 TYR B 261 ARG 0.006 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 150 LYS cc_start: 0.7480 (ttmm) cc_final: 0.7193 (ttmm) REVERT: A 213 ASP cc_start: 0.6244 (m-30) cc_final: 0.5916 (m-30) REVERT: B 81 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6855 (t0) REVERT: B 108 ASN cc_start: 0.7590 (m-40) cc_final: 0.7356 (m110) REVERT: B 123 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7140 (mtt180) REVERT: B 127 GLU cc_start: 0.6739 (mp0) cc_final: 0.6287 (mp0) REVERT: B 176 LYS cc_start: 0.6442 (tmmt) cc_final: 0.6059 (tmmt) REVERT: B 230 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6376 (mtpt) REVERT: B 267 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6833 (mmt-90) REVERT: B 285 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6353 (mmt) REVERT: B 289 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6623 (mt-10) REVERT: B 380 GLU cc_start: 0.6744 (tp30) cc_final: 0.6372 (mm-30) REVERT: B 387 SER cc_start: 0.7612 (t) cc_final: 0.7159 (m) REVERT: B 397 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 455 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7331 (p) REVERT: B 561 GLN cc_start: 0.7329 (mt0) cc_final: 0.6581 (mp10) REVERT: B 569 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.6998 (mp) REVERT: B 690 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7131 (mm-30) REVERT: C 64 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6665 (pp20) REVERT: C 68 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7729 (tp) REVERT: C 98 MET cc_start: 0.8095 (mtt) cc_final: 0.7789 (mtp) REVERT: C 229 GLU cc_start: 0.7060 (tt0) cc_final: 0.6841 (tt0) REVERT: C 243 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7589 (p90) outliers start: 28 outliers final: 15 residues processed: 166 average time/residue: 1.3760 time to fit residues: 240.6032 Evaluate side-chains 174 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.0470 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.0050 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS B 549 ASN B 554 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.7970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7957 Z= 0.215 Angle : 0.551 11.256 10759 Z= 0.268 Chirality : 0.038 0.145 1231 Planarity : 0.004 0.044 1371 Dihedral : 3.948 27.295 1046 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.38 % Allowed : 23.34 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.27), residues: 957 helix: 1.77 (0.19), residues: 698 sheet: None (None), residues: 0 loop : -0.03 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 275 HIS 0.004 0.001 HIS B 303 PHE 0.018 0.002 PHE C 243 TYR 0.011 0.001 TYR B 688 ARG 0.006 0.000 ARG B 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 150 LYS cc_start: 0.7498 (ttmm) cc_final: 0.7222 (ttmm) REVERT: A 213 ASP cc_start: 0.6246 (m-30) cc_final: 0.5907 (m-30) REVERT: B 123 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7117 (mtt180) REVERT: B 127 GLU cc_start: 0.6779 (mp0) cc_final: 0.6327 (pm20) REVERT: B 136 TYR cc_start: 0.6710 (t80) cc_final: 0.6491 (t80) REVERT: B 176 LYS cc_start: 0.6462 (tmmt) cc_final: 0.6230 (ttmt) REVERT: B 230 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6334 (mtpt) REVERT: B 267 ARG cc_start: 0.7077 (mmt180) cc_final: 0.6832 (mmt-90) REVERT: B 285 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6012 (mmt) REVERT: B 289 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6661 (mt-10) REVERT: B 329 GLN cc_start: 0.6565 (mt0) cc_final: 0.6352 (tm130) REVERT: B 380 GLU cc_start: 0.6760 (tp30) cc_final: 0.6418 (mp0) REVERT: B 387 SER cc_start: 0.7541 (t) cc_final: 0.7091 (m) REVERT: B 397 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 455 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7306 (p) REVERT: B 548 ASP cc_start: 0.7350 (t0) cc_final: 0.7076 (t0) REVERT: B 561 GLN cc_start: 0.7333 (mt0) cc_final: 0.6590 (mp10) REVERT: B 569 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7023 (mp) REVERT: B 633 CYS cc_start: 0.7389 (m) cc_final: 0.6865 (p) REVERT: C 64 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6650 (pp20) REVERT: C 68 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7693 (tp) REVERT: C 98 MET cc_start: 0.8094 (mtt) cc_final: 0.7805 (mtp) REVERT: C 229 GLU cc_start: 0.7063 (tt0) cc_final: 0.6841 (tt0) REVERT: C 243 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7585 (p90) outliers start: 29 outliers final: 16 residues processed: 164 average time/residue: 1.3476 time to fit residues: 232.8728 Evaluate side-chains 168 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.0370 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS B 108 ASN B 549 ASN B 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.146412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130380 restraints weight = 9841.556| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.59 r_work: 0.3618 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7957 Z= 0.200 Angle : 0.540 11.347 10759 Z= 0.266 Chirality : 0.038 0.140 1231 Planarity : 0.004 0.044 1371 Dihedral : 3.874 26.944 1046 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.92 % Allowed : 23.69 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 957 helix: 1.84 (0.20), residues: 699 sheet: None (None), residues: 0 loop : -0.01 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 296 HIS 0.011 0.001 HIS B 48 PHE 0.017 0.002 PHE C 243 TYR 0.010 0.001 TYR B 688 ARG 0.006 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4088.53 seconds wall clock time: 73 minutes 30.44 seconds (4410.44 seconds total)