Starting phenix.real_space_refine on Wed Mar 12 12:02:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy4_29552/03_2025/8fy4_29552.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy4_29552/03_2025/8fy4_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/cci-nas-00/data/ceres_data/8fy4_29552/03_2025/8fy4_29552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy4_29552/03_2025/8fy4_29552.map" model { file = "/net/cci-nas-00/data/ceres_data/8fy4_29552/03_2025/8fy4_29552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy4_29552/03_2025/8fy4_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 10.19, per 1000 atoms: 1.31 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: 2.37 Conformation dependent library (CDL) restraints added in 1.4 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: 0.76 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: 2.48 Time building geometry restraints manager: 2.82 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: 393.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 33.500 Find NCS groups from input model: 0.160 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:22.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 449.570 ------------------------------------------------------------------------------- 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 : 1.128 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: 1.1745 time to fit residues: 172.0140 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 : 0.845 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.164808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148286 restraints weight = 10235.343| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.56 r_work: 0.3864 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.848 Fit side-chains revert: symmetry clash REVERT: B 176 LYS cc_start: 0.6988 (tmmt) cc_final: 0.6725 (tmmt) REVERT: B 285 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5225 (mmp) REVERT: B 459 GLU cc_start: 0.7381 (mp0) cc_final: 0.7038 (mp0) REVERT: B 561 GLN cc_start: 0.7806 (mt0) cc_final: 0.7595 (mp10) REVERT: B 582 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6965 (mt) outliers start: 43 outliers final: 11 residues processed: 171 average time/residue: 1.3914 time to fit residues: 253.8400 Evaluate side-chains 134 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 125 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 554 ASN C 58 HIS C 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.152700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135970 restraints weight = 10171.343| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.61 r_work: 0.3701 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7957 Z= 0.325 Angle : 0.634 8.805 10759 Z= 0.317 Chirality : 0.041 0.162 1231 Planarity : 0.005 0.049 1371 Dihedral : 4.718 41.585 1052 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.02 % Allowed : 19.60 % Favored : 75.38 % 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: 1.51 (0.27), residues: 957 helix: 1.45 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.11 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 296 HIS 0.008 0.001 HIS C 58 PHE 0.015 0.002 PHE B 314 TYR 0.019 0.002 TYR B 688 ARG 0.005 0.001 ARG B 431 *********************** 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 192 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.797 Fit side-chains REVERT: A 77 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: B 123 ARG cc_start: 0.8166 (mpp80) cc_final: 0.7689 (mtt-85) REVERT: B 143 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6404 (tm-30) REVERT: B 176 LYS cc_start: 0.7092 (tmmt) cc_final: 0.6852 (tmmt) REVERT: B 561 GLN cc_start: 0.7853 (mt0) cc_final: 0.7614 (mp10) REVERT: B 569 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 690 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7635 (mm-30) REVERT: C 64 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6857 (pp20) REVERT: C 68 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8083 (tt) REVERT: C 150 GLN cc_start: 0.5948 (OUTLIER) cc_final: 0.5672 (pp30) REVERT: C 229 GLU cc_start: 0.7725 (tt0) cc_final: 0.7524 (tt0) outliers start: 43 outliers final: 12 residues processed: 172 average time/residue: 1.3426 time to fit residues: 243.3726 Evaluate side-chains 150 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 265 ASN 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 569 LEU Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 665 CYS 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 72 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.0470 chunk 81 optimal weight: 0.1980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 125 GLN A 151 GLN B 108 ASN B 549 ASN B 632 GLN C 58 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.151558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134708 restraints weight = 9944.452| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.60 r_work: 0.3686 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7957 Z= 0.227 Angle : 0.558 9.191 10759 Z= 0.276 Chirality : 0.039 0.150 1231 Planarity : 0.005 0.071 1371 Dihedral : 4.069 28.107 1046 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.38 % Allowed : 22.29 % Favored : 74.33 % 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: 1.81 (0.27), residues: 957 helix: 1.69 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.00 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.007 0.001 HIS C 58 PHE 0.020 0.002 PHE C 247 TYR 0.014 0.001 TYR B 355 ARG 0.007 0.001 ARG A 232 *********************** 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 180 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 2.070 Fit side-chains REVERT: B 123 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7657 (mtt180) REVERT: B 143 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6642 (tm-30) REVERT: B 176 LYS cc_start: 0.7149 (tmmt) cc_final: 0.6884 (tmmt) REVERT: B 561 GLN cc_start: 0.7876 (mt0) cc_final: 0.7619 (mp10) REVERT: B 569 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7724 (mp) REVERT: B 690 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7590 (mm-30) REVERT: C 68 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8300 (tp) REVERT: C 145 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7707 (ttpp) outliers start: 29 outliers final: 11 residues processed: 166 average time/residue: 1.8698 time to fit residues: 326.5088 Evaluate side-chains 159 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 265 ASN 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 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 145 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 0.0070 chunk 66 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 125 GLN A 151 GLN B 81 ASN B 526 GLN B 549 ASN B 554 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134104 restraints weight = 9796.396| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.58 r_work: 0.3671 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7957 Z= 0.241 Angle : 0.555 8.855 10759 Z= 0.276 Chirality : 0.038 0.148 1231 Planarity : 0.005 0.044 1371 Dihedral : 4.063 28.249 1046 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.73 % Allowed : 22.40 % Favored : 73.86 % 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: 1.74 (0.27), residues: 957 helix: 1.63 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.00 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.018 0.002 PHE C 247 TYR 0.013 0.001 TYR B 355 ARG 0.008 0.001 ARG A 232 *********************** 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 182 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.841 Fit side-chains REVERT: A 77 GLU cc_start: 0.7757 (tp30) cc_final: 0.7534 (mp0) REVERT: B 123 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7680 (mtt180) REVERT: B 176 LYS cc_start: 0.7198 (tmmt) cc_final: 0.6882 (tmmt) REVERT: B 561 GLN cc_start: 0.7775 (mt0) cc_final: 0.7564 (mp10) REVERT: B 569 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7719 (mp) REVERT: B 690 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7657 (mm-30) REVERT: C 151 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7317 (mp) REVERT: C 152 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6627 (mmt) REVERT: C 194 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7637 (mm-30) REVERT: C 243 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7876 (p90) outliers start: 32 outliers final: 12 residues processed: 165 average time/residue: 1.1387 time to fit residues: 199.4002 Evaluate side-chains 166 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER 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 123 ARG Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 455 VAL 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 151 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 83 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 76 GLN A 97 ASN A 125 GLN B 108 ASN B 549 ASN B 554 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134057 restraints weight = 9902.730| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.61 r_work: 0.3673 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6537 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= 0.185 Angle : 0.530 10.247 10759 Z= 0.259 Chirality : 0.037 0.143 1231 Planarity : 0.004 0.044 1371 Dihedral : 3.760 13.863 1044 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.15 % Allowed : 23.57 % 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: 1.94 (0.27), residues: 957 helix: 1.79 (0.20), residues: 697 sheet: None (None), residues: 0 loop : 0.01 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 296 HIS 0.004 0.001 HIS B 48 PHE 0.016 0.001 PHE C 243 TYR 0.012 0.001 TYR B 688 ARG 0.007 0.001 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 164 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.877 Fit side-chains REVERT: A 236 MET cc_start: 0.7648 (mtm) cc_final: 0.7276 (mtp) REVERT: B 123 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7759 (mtt-85) REVERT: B 176 LYS cc_start: 0.7242 (tmmt) cc_final: 0.6937 (tmmt) REVERT: B 383 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: B 561 GLN cc_start: 0.7799 (mt0) cc_final: 0.7587 (mp10) REVERT: B 569 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7763 (mp) REVERT: C 145 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7642 (ttpp) REVERT: C 152 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6641 (mmt) REVERT: C 194 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 243 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7698 (p90) outliers start: 27 outliers final: 13 residues processed: 154 average time/residue: 1.2647 time to fit residues: 205.8219 Evaluate side-chains 158 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 138 SER 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 293 CYS Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 455 VAL 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 C residue 145 LYS Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 72 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 97 ASN B 108 ASN B 148 GLN B 549 ASN B 554 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.149412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132903 restraints weight = 9950.821| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.60 r_work: 0.3656 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.6752 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= 0.221 Angle : 0.543 12.576 10759 Z= 0.265 Chirality : 0.038 0.146 1231 Planarity : 0.004 0.045 1371 Dihedral : 3.769 13.598 1044 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.27 % Allowed : 24.04 % Favored : 72.70 % 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: 1.89 (0.27), residues: 957 helix: 1.75 (0.19), residues: 697 sheet: None (None), residues: 0 loop : 0.03 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.017 0.002 PHE C 243 TYR 0.011 0.001 TYR B 355 ARG 0.005 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 167 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.794 Fit side-chains REVERT: B 123 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7759 (mtt-85) REVERT: B 383 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: B 569 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7677 (mp) REVERT: B 697 GLN cc_start: 0.6169 (pm20) cc_final: 0.5963 (pm20) REVERT: C 145 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7619 (ttpp) REVERT: C 194 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7683 (mm-30) REVERT: C 243 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7656 (p90) outliers start: 28 outliers final: 15 residues processed: 157 average time/residue: 1.1963 time to fit residues: 198.7966 Evaluate side-chains 151 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 SER 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 174 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 455 VAL 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 145 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 7 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 90 optimal weight: 0.4980 chunk 20 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 76 GLN A 97 ASN A 125 GLN B 108 ASN B 148 GLN B 549 ASN B 554 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132078 restraints weight = 9961.643| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.61 r_work: 0.3643 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7957 Z= 0.221 Angle : 0.547 11.571 10759 Z= 0.269 Chirality : 0.038 0.146 1231 Planarity : 0.004 0.045 1371 Dihedral : 3.761 14.131 1044 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.50 % Allowed : 24.27 % Favored : 72.23 % 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: 1.84 (0.27), residues: 957 helix: 1.70 (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 0.008 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.017 0.002 PHE C 243 TYR 0.011 0.001 TYR B 355 ARG 0.004 0.000 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 169 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.788 Fit side-chains REVERT: B 123 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7740 (mtt-85) REVERT: B 383 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: B 569 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7689 (mp) REVERT: C 145 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7641 (ttpp) REVERT: C 243 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7606 (p90) outliers start: 30 outliers final: 17 residues processed: 158 average time/residue: 1.2405 time to fit residues: 207.7287 Evaluate side-chains 164 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 138 SER Chi-restraints excluded: chain A residue 183 LEU 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 174 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 455 VAL 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 703 ILE Chi-restraints excluded: chain C residue 145 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.0980 chunk 68 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 54 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 76 GLN A 97 ASN B 65 ASN B 108 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 554 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131783 restraints weight = 9996.191| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.61 r_work: 0.3639 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.7215 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= 0.228 Angle : 0.553 11.161 10759 Z= 0.272 Chirality : 0.039 0.201 1231 Planarity : 0.004 0.045 1371 Dihedral : 3.787 14.631 1044 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.38 % Allowed : 24.50 % Favored : 72.11 % 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: 1.80 (0.27), residues: 957 helix: 1.66 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.05 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.017 0.002 PHE C 243 TYR 0.011 0.001 TYR B 355 ARG 0.004 0.000 ARG B 354 *********************** 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 177 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.861 Fit side-chains REVERT: A 150 LYS cc_start: 0.8292 (ttmm) cc_final: 0.8091 (ttmm) REVERT: B 123 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7737 (mtt-85) REVERT: B 383 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: B 455 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 569 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7688 (mp) REVERT: C 145 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7608 (ttpp) REVERT: C 243 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7626 (p90) outliers start: 29 outliers final: 16 residues processed: 167 average time/residue: 1.2860 time to fit residues: 226.7494 Evaluate side-chains 168 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 SER 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 174 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 455 VAL 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 C residue 145 LYS 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 83 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 55 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 76 GLN A 97 ASN A 151 GLN B 108 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 549 ASN B 554 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.147895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131504 restraints weight = 9947.715| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.60 r_work: 0.3635 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7957 Z= 0.220 Angle : 0.557 10.914 10759 Z= 0.275 Chirality : 0.039 0.187 1231 Planarity : 0.004 0.045 1371 Dihedral : 3.776 15.290 1044 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.27 % Allowed : 25.09 % Favored : 71.65 % 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: 1.86 (0.27), residues: 957 helix: 1.71 (0.19), residues: 696 sheet: None (None), residues: 0 loop : 0.07 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.017 0.002 PHE C 243 TYR 0.013 0.001 TYR B 355 ARG 0.005 0.000 ARG B 354 ********************** 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 165 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.837 Fit side-chains REVERT: B 123 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7763 (mtt-85) REVERT: B 383 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: B 455 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8137 (p) REVERT: B 569 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7670 (mp) REVERT: C 145 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7609 (ttpp) REVERT: C 243 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7629 (p90) outliers start: 28 outliers final: 14 residues processed: 154 average time/residue: 1.2528 time to fit residues: 203.9497 Evaluate side-chains 162 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 151 GLN 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 293 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 455 VAL 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 C residue 137 LEU Chi-restraints excluded: chain C residue 145 LYS 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 34 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 0.0010 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN A 151 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 554 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131463 restraints weight = 9955.677| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.60 r_work: 0.3634 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.7399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.187 7957 Z= 0.441 Angle : 1.192 59.169 10759 Z= 0.716 Chirality : 0.055 1.281 1231 Planarity : 0.005 0.050 1371 Dihedral : 3.930 28.255 1044 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.68 % Allowed : 25.79 % Favored : 71.53 % Cbeta Deviations : 0.21 % 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: 1.82 (0.27), residues: 957 helix: 1.67 (0.19), residues: 696 sheet: None (None), residues: 0 loop : 0.08 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.017 0.001 PHE C 243 TYR 0.013 0.001 TYR B 355 ARG 0.004 0.000 ARG B 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7369.94 seconds wall clock time: 128 minutes 4.47 seconds (7684.47 seconds total)