Starting phenix.real_space_refine on Wed Feb 12 11:42:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy4_29552/02_2025/8fy4_29552.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy4_29552/02_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_29552/02_2025/8fy4_29552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy4_29552/02_2025/8fy4_29552.map" model { file = "/net/cci-nas-00/data/ceres_data/8fy4_29552/02_2025/8fy4_29552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy4_29552/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.85, per 1000 atoms: 0.75 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: 1.95 Conformation dependent library (CDL) restraints added in 1.0 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: 0.83 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: 2.24 Time building geometry restraints manager: 2.30 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.920 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- 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 : 0.856 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: 1.2465 time to fit residues: 182.2800 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 : 0.881 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148273 restraints weight = 10235.335| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.56 r_work: 0.3864 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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 : 0.914 Fit side-chains revert: symmetry clash REVERT: B 176 LYS cc_start: 0.6989 (tmmt) cc_final: 0.6727 (tmmt) REVERT: B 285 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5226 (mmp) REVERT: B 459 GLU cc_start: 0.7381 (mp0) cc_final: 0.7036 (mp0) REVERT: B 561 GLN cc_start: 0.7806 (mt0) cc_final: 0.7593 (mp10) REVERT: B 582 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6966 (mt) outliers start: 43 outliers final: 11 residues processed: 171 average time/residue: 1.2501 time to fit residues: 226.5648 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 : 0.847 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 54 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 114 GLN A 125 GLN A 200 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4004 r_free = 0.4004 target = 0.151457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134680 restraints weight = 10121.353| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.60 r_work: 0.3684 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 7957 Z= 0.355 Angle : 0.661 8.450 10759 Z= 0.334 Chirality : 0.042 0.168 1231 Planarity : 0.005 0.046 1371 Dihedral : 4.808 41.544 1052 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.90 % Allowed : 19.49 % Favored : 75.61 % 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: 1.41 (0.27), residues: 957 helix: 1.38 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -0.13 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 296 HIS 0.008 0.001 HIS C 58 PHE 0.016 0.002 PHE B 314 TYR 0.021 0.002 TYR B 688 ARG 0.005 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 197 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.893 Fit side-chains REVERT: A 76 GLN cc_start: 0.7897 (tt0) cc_final: 0.7696 (tt0) REVERT: A 77 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: B 123 ARG cc_start: 0.8201 (mpp80) cc_final: 0.7718 (mtt-85) REVERT: B 143 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6486 (tm-30) REVERT: B 176 LYS cc_start: 0.7119 (tmmt) cc_final: 0.6870 (tmmt) REVERT: B 268 LYS cc_start: 0.7445 (ttpt) cc_final: 0.7220 (tttp) REVERT: B 561 GLN cc_start: 0.7852 (mt0) cc_final: 0.7609 (mp10) REVERT: B 569 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7711 (mp) REVERT: B 690 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 64 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6894 (pp20) REVERT: C 68 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8147 (tt) REVERT: C 150 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5801 (pp30) outliers start: 42 outliers final: 11 residues processed: 179 average time/residue: 1.3304 time to fit residues: 251.1297 Evaluate side-chains 154 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 138 SER 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 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 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: 0.9980 chunk 2 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 216 GLN B 81 ASN B 108 ASN B 526 GLN B 549 ASN B 554 ASN B 632 GLN C 58 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.149636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132825 restraints weight = 9916.991| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.61 r_work: 0.3661 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7957 Z= 0.278 Angle : 0.583 9.507 10759 Z= 0.290 Chirality : 0.040 0.158 1231 Planarity : 0.005 0.071 1371 Dihedral : 4.193 29.095 1046 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.32 % Allowed : 21.35 % 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: 1.53 (0.27), residues: 957 helix: 1.51 (0.19), residues: 701 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.008 0.001 HIS C 58 PHE 0.022 0.002 PHE C 247 TYR 0.013 0.002 TYR B 355 ARG 0.027 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 193 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.885 Fit side-chains REVERT: B 123 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7755 (mtt-85) REVERT: B 174 LEU cc_start: 0.7365 (tp) cc_final: 0.7138 (tp) REVERT: B 176 LYS cc_start: 0.7182 (tmmt) cc_final: 0.6885 (tmmt) REVERT: B 265 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7699 (p0) REVERT: B 291 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7506 (mp) REVERT: B 561 GLN cc_start: 0.7862 (mt0) cc_final: 0.7625 (mp10) REVERT: B 569 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7740 (mp) REVERT: B 690 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7601 (mm-30) REVERT: C 68 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8361 (tp) REVERT: C 145 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7712 (ttpp) outliers start: 37 outliers final: 9 residues processed: 178 average time/residue: 1.3296 time to fit residues: 249.1337 Evaluate side-chains 168 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 265 ASN Chi-restraints excluded: chain B residue 291 LEU 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 665 CYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 137 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: 0.9990 chunk 19 optimal weight: 0.0470 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 97 ASN A 125 GLN A 216 GLN B 108 ASN B 310 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 = 0.3978 r_free = 0.3978 target = 0.149821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133269 restraints weight = 9776.451| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.58 r_work: 0.3664 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.6529 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= 0.213 Angle : 0.547 9.364 10759 Z= 0.272 Chirality : 0.037 0.147 1231 Planarity : 0.005 0.044 1371 Dihedral : 4.058 28.789 1046 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.20 % Allowed : 22.99 % Favored : 72.81 % 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: 1.70 (0.19), residues: 693 sheet: None (None), residues: 0 loop : 0.04 (0.40), residues: 264 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 0.017 0.002 PHE C 243 TYR 0.013 0.001 TYR B 355 ARG 0.007 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 178 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.794 Fit side-chains REVERT: B 123 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7752 (mtt-85) REVERT: B 176 LYS cc_start: 0.7221 (tmmt) cc_final: 0.6917 (tmmt) REVERT: B 561 GLN cc_start: 0.7818 (mt0) cc_final: 0.7587 (mp10) REVERT: B 569 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7748 (mp) REVERT: C 145 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7654 (ttpp) REVERT: C 152 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6599 (mmt) REVERT: C 194 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7591 (mm-30) outliers start: 36 outliers final: 14 residues processed: 162 average time/residue: 1.2314 time to fit residues: 211.2982 Evaluate side-chains 160 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain B residue 123 ARG 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 73 optimal weight: 0.0370 chunk 52 optimal weight: 0.3980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 216 GLN B 108 ASN B 388 ASN 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 = 0.3975 r_free = 0.3975 target = 0.149544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132880 restraints weight = 9880.382| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.61 r_work: 0.3659 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7957 Z= 0.197 Angle : 0.527 10.153 10759 Z= 0.259 Chirality : 0.037 0.143 1231 Planarity : 0.004 0.044 1371 Dihedral : 3.802 13.939 1044 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.20 % Allowed : 22.75 % Favored : 73.05 % 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: 1.96 (0.27), residues: 957 helix: 1.79 (0.20), residues: 695 sheet: None (None), residues: 0 loop : 0.08 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.016 0.001 PHE C 247 TYR 0.013 0.001 TYR B 355 ARG 0.005 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 187 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.880 Fit side-chains REVERT: B 71 PHE cc_start: 0.6752 (t80) cc_final: 0.6459 (t80) REVERT: B 123 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7746 (mtt-85) REVERT: B 174 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7060 (tp) REVERT: B 176 LYS cc_start: 0.7281 (tmmt) cc_final: 0.6982 (tmmt) REVERT: B 561 GLN cc_start: 0.7804 (mt0) cc_final: 0.7585 (mp10) REVERT: B 569 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7732 (mp) REVERT: C 145 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7632 (ttpp) REVERT: C 152 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6612 (mmt) REVERT: C 194 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7640 (mm-30) outliers start: 36 outliers final: 17 residues processed: 173 average time/residue: 1.2864 time to fit residues: 235.1796 Evaluate side-chains 170 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 243 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 382 VAL 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 704 LYS 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 197 THR 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 97 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 216 GLN B 65 ASN B 108 ASN B 449 GLN B 554 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.145315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129394 restraints weight = 9983.645| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.56 r_work: 0.3602 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.7511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 7957 Z= 0.370 Angle : 0.639 12.147 10759 Z= 0.313 Chirality : 0.043 0.160 1231 Planarity : 0.005 0.044 1371 Dihedral : 4.223 14.358 1044 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.08 % Allowed : 22.75 % Favored : 73.16 % 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: 1.43 (0.27), residues: 957 helix: 1.38 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.07 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 296 HIS 0.007 0.001 HIS B 303 PHE 0.021 0.002 PHE C 247 TYR 0.016 0.002 TYR B 261 ARG 0.017 0.001 ARG B 263 *********************** 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 178 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.924 Fit side-chains REVERT: B 123 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7802 (mtt-85) REVERT: B 176 LYS cc_start: 0.7358 (tmmt) cc_final: 0.7051 (tmmt) REVERT: B 459 GLU cc_start: 0.7759 (mp0) cc_final: 0.7551 (mp0) REVERT: B 561 GLN cc_start: 0.7783 (mt0) cc_final: 0.7552 (mp10) REVERT: B 569 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7931 (mp) outliers start: 35 outliers final: 15 residues processed: 165 average time/residue: 1.2728 time to fit residues: 224.3232 Evaluate side-chains 153 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 B residue 52 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 382 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 C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 226 GLN 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: 0.3980 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 216 GLN B 108 ASN B 449 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 = 0.3941 r_free = 0.3941 target = 0.146816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130766 restraints weight = 9938.089| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.59 r_work: 0.3621 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.7650 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= 0.225 Angle : 0.558 10.896 10759 Z= 0.274 Chirality : 0.039 0.149 1231 Planarity : 0.004 0.045 1371 Dihedral : 3.946 16.627 1044 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.62 % Allowed : 23.69 % 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: 1.74 (0.27), residues: 957 helix: 1.65 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.07 (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 0.016 0.001 PHE C 247 TYR 0.012 0.001 TYR B 136 ARG 0.007 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 183 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.900 Fit side-chains REVERT: A 77 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: A 236 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7496 (mtm) REVERT: B 123 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: B 176 LYS cc_start: 0.7428 (tmmt) cc_final: 0.7087 (tmmt) REVERT: B 561 GLN cc_start: 0.7801 (mt0) cc_final: 0.7547 (mp10) REVERT: B 569 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 690 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7932 (mm-30) REVERT: C 243 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7616 (p90) outliers start: 31 outliers final: 13 residues processed: 172 average time/residue: 1.3203 time to fit residues: 239.4968 Evaluate side-chains 157 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 236 MET 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 243 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 382 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 665 CYS 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: 0.8980 chunk 68 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 54 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 125 GLN A 216 GLN B 108 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130183 restraints weight = 9959.744| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.59 r_work: 0.3613 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7957 Z= 0.250 Angle : 0.577 10.435 10759 Z= 0.284 Chirality : 0.040 0.148 1231 Planarity : 0.004 0.044 1371 Dihedral : 3.949 17.006 1044 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.27 % Allowed : 24.27 % Favored : 72.46 % 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: 1.71 (0.27), residues: 957 helix: 1.63 (0.19), residues: 697 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 296 HIS 0.005 0.001 HIS B 303 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 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 169 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 236 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7497 (mtm) REVERT: B 123 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7694 (mtt180) REVERT: B 176 LYS cc_start: 0.7408 (tmmt) cc_final: 0.7060 (tmmt) REVERT: B 215 LYS cc_start: 0.7689 (mmtm) cc_final: 0.7487 (mttm) REVERT: B 569 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 690 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7926 (mm-30) REVERT: C 243 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7627 (p90) outliers start: 28 outliers final: 17 residues processed: 161 average time/residue: 1.2970 time to fit residues: 220.6583 Evaluate side-chains 159 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 236 MET 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 243 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 382 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 665 CYS Chi-restraints excluded: chain B residue 676 LYS 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 Chi-restraints excluded: chain C residue 254 LEU 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: 0.5980 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 96 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS B 48 HIS B 108 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.130577 restraints weight = 9887.258| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.57 r_work: 0.3620 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.7913 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= 0.237 Angle : 0.579 10.810 10759 Z= 0.285 Chirality : 0.040 0.145 1231 Planarity : 0.004 0.044 1371 Dihedral : 3.944 18.175 1044 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.10 % Allowed : 25.79 % 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: 1.75 (0.27), residues: 957 helix: 1.65 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -0.08 (0.41), residues: 257 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 247 TYR 0.011 0.001 TYR B 136 ARG 0.006 0.001 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 161 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.860 Fit side-chains REVERT: A 77 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 150 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7963 (ttmm) REVERT: A 236 MET cc_start: 0.7762 (mtp) cc_final: 0.7449 (mtm) REVERT: B 123 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7815 (mtt-85) REVERT: B 152 PHE cc_start: 0.7817 (m-10) cc_final: 0.7604 (m-10) REVERT: B 176 LYS cc_start: 0.7402 (tmmt) cc_final: 0.7117 (ttmt) REVERT: B 569 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7663 (mp) REVERT: B 690 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7917 (mm-30) REVERT: C 243 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7618 (p90) REVERT: C 254 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7890 (mp) outliers start: 18 outliers final: 11 residues processed: 156 average time/residue: 1.2863 time to fit residues: 211.5817 Evaluate side-chains 154 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 382 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 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 Chi-restraints excluded: chain C residue 254 LEU 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: 1.9990 chunk 33 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 2 optimal weight: 0.2980 chunk 66 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS B 48 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 554 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.146106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.130356 restraints weight = 9883.491| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.57 r_work: 0.3618 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.8012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7957 Z= 0.242 Angle : 0.582 10.276 10759 Z= 0.288 Chirality : 0.040 0.145 1231 Planarity : 0.004 0.044 1371 Dihedral : 3.943 18.549 1044 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.45 % Allowed : 25.55 % Favored : 72.00 % 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: 1.78 (0.27), residues: 957 helix: 1.68 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -0.07 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 96 HIS 0.004 0.001 HIS B 303 PHE 0.017 0.002 PHE C 247 TYR 0.010 0.001 TYR B 688 ARG 0.007 0.001 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6644.46 seconds wall clock time: 117 minutes 42.20 seconds (7062.20 seconds total)