Starting phenix.real_space_refine on Fri Feb 14 05:35:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fn4_3239/02_2025/5fn4_3239.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fn4_3239/02_2025/5fn4_3239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5fn4_3239/02_2025/5fn4_3239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fn4_3239/02_2025/5fn4_3239.map" model { file = "/net/cci-nas-00/data/ceres_data/5fn4_3239/02_2025/5fn4_3239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fn4_3239/02_2025/5fn4_3239.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 35 5.16 5 C 6398 2.51 5 N 1596 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9776 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 235} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 5.67, per 1000 atoms: 0.58 Number of scatterers: 9776 At special positions: 0 Unit cell: (91, 142.8, 103.6, 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 35 16.00 O 1747 8.00 N 1596 7.00 C 6398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.01 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.05 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 60.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.354A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.862A pdb=" N CYS A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.640A pdb=" N ASN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.829A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.651A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.530A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.775A pdb=" N TYR A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.901A pdb=" N LEU A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 104 Proline residue: B 88 - end of helix removed outlier: 4.039A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.533A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 241 Processing helix chain 'B' and resid 242 through 262 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 428 removed outlier: 3.503A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.420A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.626A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 100 removed outlier: 4.077A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.864A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.874A pdb=" N THR C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 4.295A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 213 through 232 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.704A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 4.207A pdb=" N ARG D 5 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 26 through 43 removed outlier: 4.312A pdb=" N TRP D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 85 Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'G' and resid -1 through 23 Processing sheet with id=AA, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.673A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AC, first strand: chain 'A' and resid 72 through 76 removed outlier: 4.425A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.635A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.172A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.858A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1737 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: 3.11 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1685 1.32 - 1.45: 2759 1.45 - 1.57: 5523 1.57 - 1.70: 8 1.70 - 1.82: 53 Bond restraints: 10028 Sorted by residual: bond pdb=" C LEU C 244 " pdb=" O LEU C 244 " ideal model delta sigma weight residual 1.231 1.380 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C HIS C 197 " pdb=" O HIS C 197 " ideal model delta sigma weight residual 1.236 1.304 -0.067 1.15e-02 7.56e+03 3.42e+01 bond pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 1.539 1.562 -0.023 5.40e-03 3.43e+04 1.77e+01 bond pdb=" CA VAL B 255 " pdb=" CB VAL B 255 " ideal model delta sigma weight residual 1.540 1.582 -0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.17e-02 7.31e+03 1.28e+01 ... (remaining 10023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 11458 2.48 - 4.96: 2064 4.96 - 7.44: 121 7.44 - 9.92: 26 9.92 - 12.40: 6 Bond angle restraints: 13675 Sorted by residual: angle pdb=" O ALA G 22 " pdb=" C ALA G 22 " pdb=" N ALA G 23 " ideal model delta sigma weight residual 122.07 109.70 12.37 1.03e+00 9.43e-01 1.44e+02 angle pdb=" O ALA G 21 " pdb=" C ALA G 21 " pdb=" N ALA G 22 " ideal model delta sigma weight residual 122.07 109.73 12.34 1.03e+00 9.43e-01 1.44e+02 angle pdb=" N ILE A 162 " pdb=" CA ILE A 162 " pdb=" C ILE A 162 " ideal model delta sigma weight residual 111.62 118.93 -7.31 7.90e-01 1.60e+00 8.55e+01 angle pdb=" O VAL B 87 " pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 120.42 125.11 -4.69 6.40e-01 2.44e+00 5.38e+01 angle pdb=" CA LEU C 169 " pdb=" C LEU C 169 " pdb=" N LEU C 170 " ideal model delta sigma weight residual 117.07 108.87 8.20 1.14e+00 7.69e-01 5.18e+01 ... (remaining 13670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4964 17.74 - 35.47: 643 35.47 - 53.21: 188 53.21 - 70.95: 44 70.95 - 88.68: 12 Dihedral angle restraints: 5851 sinusoidal: 2208 harmonic: 3643 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual 93.00 168.51 -75.51 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 162.50 -69.50 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 5848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1310 0.120 - 0.240: 235 0.240 - 0.360: 30 0.360 - 0.480: 8 0.480 - 0.600: 1 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" CA PHE A 218 " pdb=" N PHE A 218 " pdb=" C PHE A 218 " pdb=" CB PHE A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA LEU A 312 " pdb=" N LEU A 312 " pdb=" C LEU A 312 " pdb=" CB LEU A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 1581 not shown) Planarity restraints: 1706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 21 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C ALA G 21 " 0.216 2.00e-02 2.50e+03 pdb=" O ALA G 21 " -0.080 2.00e-02 2.50e+03 pdb=" N ALA G 22 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 22 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.55e+02 pdb=" C ALA G 22 " 0.216 2.00e-02 2.50e+03 pdb=" O ALA G 22 " -0.080 2.00e-02 2.50e+03 pdb=" N ALA G 23 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 175 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C PHE B 175 " -0.073 2.00e-02 2.50e+03 pdb=" O PHE B 175 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE B 176 " 0.025 2.00e-02 2.50e+03 ... (remaining 1703 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 180 2.69 - 3.24: 10256 3.24 - 3.79: 16234 3.79 - 4.35: 20802 4.35 - 4.90: 32959 Nonbonded interactions: 80431 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG SER C 124 " model vdw 2.131 3.040 nonbonded pdb=" O HIS C 197 " pdb=" OG1 THR C 200 " model vdw 2.252 3.040 nonbonded pdb=" O PHE B 445 " pdb=" OG1 THR B 449 " model vdw 2.267 3.040 nonbonded pdb=" O ALA C 76 " pdb=" OG SER C 79 " model vdw 2.277 3.040 nonbonded pdb=" O ARG A 232 " pdb=" OG SER A 235 " model vdw 2.294 3.040 ... (remaining 80426 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.080 Process input model: 24.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 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 : 0.010 0.149 10028 Z= 0.644 Angle : 1.713 12.399 13675 Z= 1.236 Chirality : 0.096 0.600 1584 Planarity : 0.009 0.125 1706 Dihedral : 18.066 88.682 3484 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 3.24 % Allowed : 11.98 % Favored : 84.78 % Rotamer: Outliers : 10.51 % Allowed : 14.90 % Favored : 74.59 % Cbeta Deviations : 1.45 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 3.64 % 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: -1.44 (0.21), residues: 1235 helix: 1.03 (0.16), residues: 712 sheet: -3.69 (0.40), residues: 110 loop : -3.87 (0.25), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 36 HIS 0.017 0.003 HIS A 553 PHE 0.044 0.004 PHE B 176 TYR 0.043 0.004 TYR C 69 ARG 0.006 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 316 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.9434 (mt) cc_final: 0.9226 (mt) REVERT: A 95 MET cc_start: 0.8348 (mmt) cc_final: 0.7925 (mmm) REVERT: A 100 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 215 MET cc_start: 0.8953 (ttp) cc_final: 0.8743 (ptm) REVERT: A 217 LEU cc_start: 0.8876 (tt) cc_final: 0.8541 (pt) REVERT: A 231 MET cc_start: 0.8855 (mmp) cc_final: 0.8583 (mmm) REVERT: A 249 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: A 259 MET cc_start: 0.9163 (tpp) cc_final: 0.8757 (mmm) REVERT: A 331 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7703 (tp40) REVERT: A 347 MET cc_start: 0.9318 (mtm) cc_final: 0.9057 (mpp) REVERT: A 362 PHE cc_start: 0.8225 (t80) cc_final: 0.7950 (t80) REVERT: A 474 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8837 (pp20) REVERT: A 543 ARG cc_start: 0.8527 (ptm-80) cc_final: 0.7886 (tpt170) REVERT: A 548 ASP cc_start: 0.9101 (t0) cc_final: 0.8835 (m-30) REVERT: A 574 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 575 THR cc_start: 0.7571 (p) cc_final: 0.7207 (p) REVERT: A 649 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.6472 (t) REVERT: B 93 MET cc_start: 0.9294 (mtm) cc_final: 0.9071 (mmt) REVERT: B 106 TYR cc_start: 0.8629 (m-80) cc_final: 0.8246 (m-80) REVERT: B 167 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6393 (tp) REVERT: B 184 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8585 (mm-30) REVERT: B 223 GLN cc_start: 0.8384 (mt0) cc_final: 0.7849 (mm-40) REVERT: B 244 TRP cc_start: 0.5553 (OUTLIER) cc_final: 0.4638 (m100) REVERT: B 389 TYR cc_start: 0.8875 (m-80) cc_final: 0.8174 (m-80) REVERT: B 399 THR cc_start: 0.7568 (m) cc_final: 0.7333 (t) REVERT: B 419 CYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9010 (m) REVERT: B 456 PHE cc_start: 0.9405 (t80) cc_final: 0.9175 (t80) REVERT: C 24 THR cc_start: 0.9022 (m) cc_final: 0.8773 (p) REVERT: C 53 TRP cc_start: 0.8627 (t60) cc_final: 0.7886 (t60) REVERT: C 91 TYR cc_start: 0.8963 (t80) cc_final: 0.8735 (t80) REVERT: C 99 GLU cc_start: 0.8916 (pt0) cc_final: 0.8684 (pt0) REVERT: D 84 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8485 (mpt-90) REVERT: D 95 THR cc_start: 0.8328 (m) cc_final: 0.8011 (p) outliers start: 110 outliers final: 34 residues processed: 384 average time/residue: 0.2133 time to fit residues: 114.9887 Evaluate side-chains 262 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 85 TRP Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 305 GLN A 355 GLN A 417 ASN A 428 GLN A 450 ASN A 478 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN B 223 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057826 restraints weight = 48284.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059554 restraints weight = 27492.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060723 restraints weight = 18122.854| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10028 Z= 0.235 Angle : 0.839 10.853 13675 Z= 0.422 Chirality : 0.046 0.209 1584 Planarity : 0.006 0.061 1706 Dihedral : 9.999 66.372 1420 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 1.38 % Allowed : 7.77 % Favored : 90.85 % Rotamer: Outliers : 6.30 % Allowed : 20.15 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1235 helix: 2.60 (0.19), residues: 716 sheet: -3.18 (0.37), residues: 119 loop : -3.39 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 36 HIS 0.012 0.002 HIS A 553 PHE 0.031 0.002 PHE A 302 TYR 0.021 0.002 TYR A 565 ARG 0.004 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.2647 (t80) cc_final: 0.1989 (t80) REVERT: A 186 GLU cc_start: 0.9086 (tt0) cc_final: 0.8728 (tp30) REVERT: A 249 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: A 325 VAL cc_start: 0.9605 (t) cc_final: 0.9312 (t) REVERT: A 343 MET cc_start: 0.8820 (tpp) cc_final: 0.8509 (tpt) REVERT: A 362 PHE cc_start: 0.8732 (t80) cc_final: 0.7568 (t80) REVERT: A 378 MET cc_start: 0.8155 (mpt) cc_final: 0.7435 (mpp) REVERT: A 413 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8829 (tt) REVERT: A 428 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: A 526 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9014 (tp) REVERT: A 546 LEU cc_start: 0.9451 (mt) cc_final: 0.9209 (mt) REVERT: A 548 ASP cc_start: 0.8982 (t0) cc_final: 0.8687 (m-30) REVERT: B 168 ILE cc_start: 0.7494 (mm) cc_final: 0.7216 (mm) REVERT: B 184 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8957 (mm-30) REVERT: B 203 TRP cc_start: 0.9208 (t-100) cc_final: 0.8866 (t-100) REVERT: B 223 GLN cc_start: 0.8527 (mt0) cc_final: 0.7846 (mm-40) REVERT: B 244 TRP cc_start: 0.5016 (OUTLIER) cc_final: 0.4730 (m100) REVERT: B 412 VAL cc_start: 0.9633 (t) cc_final: 0.9420 (p) REVERT: B 441 PHE cc_start: 0.8758 (m-80) cc_final: 0.8443 (m-80) REVERT: B 458 ASP cc_start: 0.9079 (t0) cc_final: 0.8822 (m-30) REVERT: C 43 LEU cc_start: 0.9362 (mt) cc_final: 0.8970 (mt) REVERT: C 69 TYR cc_start: 0.8670 (t80) cc_final: 0.8451 (t80) REVERT: C 83 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8662 (mm-40) REVERT: C 93 LEU cc_start: 0.9255 (mt) cc_final: 0.8974 (tt) REVERT: C 127 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9249 (mp) REVERT: D 20 LEU cc_start: 0.8389 (mt) cc_final: 0.8135 (pp) REVERT: D 38 PHE cc_start: 0.8554 (t80) cc_final: 0.8301 (t80) REVERT: D 62 VAL cc_start: 0.8687 (t) cc_final: 0.8452 (m) REVERT: D 76 THR cc_start: 0.8954 (m) cc_final: 0.8711 (p) outliers start: 66 outliers final: 30 residues processed: 307 average time/residue: 0.1900 time to fit residues: 85.5872 Evaluate side-chains 230 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 23 optimal weight: 0.0050 chunk 47 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 305 GLN A 313 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 535 GLN A 606 GLN B 190 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054165 restraints weight = 51058.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055747 restraints weight = 28906.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056832 restraints weight = 19130.350| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 10028 Z= 0.420 Angle : 0.865 20.464 13675 Z= 0.439 Chirality : 0.047 0.304 1584 Planarity : 0.006 0.066 1706 Dihedral : 8.392 63.088 1379 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.50 % Favored : 90.53 % Rotamer: Outliers : 7.74 % Allowed : 21.39 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1235 helix: 1.88 (0.19), residues: 712 sheet: -3.17 (0.36), residues: 124 loop : -3.20 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 174 HIS 0.008 0.002 HIS A 553 PHE 0.040 0.003 PHE B 465 TYR 0.025 0.002 TYR B 225 ARG 0.004 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 198 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.2954 (t80) cc_final: 0.1769 (t80) REVERT: A 186 GLU cc_start: 0.8988 (tt0) cc_final: 0.8732 (tp30) REVERT: A 221 MET cc_start: 0.8832 (mmp) cc_final: 0.8059 (tpp) REVERT: A 253 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6746 (p0) REVERT: A 259 MET cc_start: 0.9107 (mmm) cc_final: 0.8644 (tpt) REVERT: A 343 MET cc_start: 0.8922 (tpp) cc_final: 0.8651 (tpt) REVERT: A 362 PHE cc_start: 0.8861 (t80) cc_final: 0.8194 (t80) REVERT: A 378 MET cc_start: 0.8281 (mpt) cc_final: 0.7629 (mpp) REVERT: A 413 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8832 (tt) REVERT: A 526 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9394 (mm) REVERT: A 546 LEU cc_start: 0.9526 (mt) cc_final: 0.9243 (mt) REVERT: A 548 ASP cc_start: 0.9060 (t0) cc_final: 0.8705 (m-30) REVERT: B 203 TRP cc_start: 0.9036 (t-100) cc_final: 0.8785 (t-100) REVERT: B 244 TRP cc_start: 0.5399 (OUTLIER) cc_final: 0.4989 (m100) REVERT: B 399 THR cc_start: 0.8377 (m) cc_final: 0.8092 (t) REVERT: B 441 PHE cc_start: 0.8962 (m-80) cc_final: 0.8652 (m-80) REVERT: B 458 ASP cc_start: 0.8958 (t0) cc_final: 0.8701 (m-30) REVERT: C 43 LEU cc_start: 0.9526 (mt) cc_final: 0.9141 (mt) REVERT: C 83 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8440 (mm-40) REVERT: C 93 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8988 (tt) REVERT: C 112 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8043 (tp) REVERT: C 114 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7773 (tp) REVERT: C 135 ILE cc_start: 0.9598 (tp) cc_final: 0.9266 (pt) REVERT: C 138 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9419 (mt) REVERT: D 18 TYR cc_start: 0.8234 (m-80) cc_final: 0.7975 (m-80) REVERT: D 38 PHE cc_start: 0.8637 (t80) cc_final: 0.8409 (t80) outliers start: 81 outliers final: 50 residues processed: 250 average time/residue: 0.1720 time to fit residues: 64.7438 Evaluate side-chains 236 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 640 TRP Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 0.4980 chunk 62 optimal weight: 0.0170 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 454 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.056000 restraints weight = 48322.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057587 restraints weight = 27307.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058648 restraints weight = 17822.805| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10028 Z= 0.255 Angle : 0.779 11.974 13675 Z= 0.384 Chirality : 0.045 0.311 1584 Planarity : 0.005 0.062 1706 Dihedral : 7.534 58.321 1368 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.21 % Favored : 91.98 % Rotamer: Outliers : 6.02 % Allowed : 23.69 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1235 helix: 1.87 (0.19), residues: 710 sheet: -2.72 (0.39), residues: 125 loop : -2.96 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 174 HIS 0.005 0.001 HIS A 553 PHE 0.039 0.002 PHE B 465 TYR 0.022 0.002 TYR A 554 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7036 (pt) REVERT: A 173 TYR cc_start: 0.2791 (t80) cc_final: 0.1374 (t80) REVERT: A 186 GLU cc_start: 0.8924 (tt0) cc_final: 0.8709 (tp30) REVERT: A 221 MET cc_start: 0.8862 (mmp) cc_final: 0.8533 (mmp) REVERT: A 253 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6840 (p0) REVERT: A 259 MET cc_start: 0.9019 (mmm) cc_final: 0.8659 (tpt) REVERT: A 378 MET cc_start: 0.8274 (mpt) cc_final: 0.7551 (mpp) REVERT: A 413 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8768 (tt) REVERT: A 546 LEU cc_start: 0.9456 (mt) cc_final: 0.9232 (mt) REVERT: A 548 ASP cc_start: 0.8875 (t0) cc_final: 0.8564 (m-30) REVERT: B 181 TYR cc_start: 0.9450 (t80) cc_final: 0.9108 (t80) REVERT: B 223 GLN cc_start: 0.8409 (mt0) cc_final: 0.7686 (mm-40) REVERT: B 399 THR cc_start: 0.8339 (m) cc_final: 0.7983 (t) REVERT: B 441 PHE cc_start: 0.9072 (m-80) cc_final: 0.8802 (m-80) REVERT: B 453 VAL cc_start: 0.9336 (t) cc_final: 0.9044 (t) REVERT: B 457 MET cc_start: 0.8245 (ptt) cc_final: 0.8015 (ptt) REVERT: B 458 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8758 (m-30) REVERT: C 41 PHE cc_start: 0.8991 (m-80) cc_final: 0.8759 (m-10) REVERT: C 43 LEU cc_start: 0.9499 (mt) cc_final: 0.9291 (mt) REVERT: C 83 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8413 (mm-40) REVERT: C 93 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8843 (tt) REVERT: C 112 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8182 (tp) REVERT: C 114 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8235 (tp) REVERT: C 135 ILE cc_start: 0.9617 (tp) cc_final: 0.9209 (pt) REVERT: C 210 TYR cc_start: 0.8753 (m-80) cc_final: 0.8511 (m-80) REVERT: D 38 PHE cc_start: 0.8572 (t80) cc_final: 0.8346 (t80) REVERT: D 76 THR cc_start: 0.8822 (m) cc_final: 0.8602 (p) outliers start: 63 outliers final: 38 residues processed: 238 average time/residue: 0.1849 time to fit residues: 66.0708 Evaluate side-chains 226 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 14 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.064375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053840 restraints weight = 50026.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055395 restraints weight = 28550.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056457 restraints weight = 18774.690| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10028 Z= 0.373 Angle : 0.793 12.167 13675 Z= 0.404 Chirality : 0.045 0.309 1584 Planarity : 0.006 0.062 1706 Dihedral : 7.074 58.786 1364 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.58 % Favored : 90.61 % Rotamer: Outliers : 7.16 % Allowed : 24.74 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1235 helix: 1.65 (0.19), residues: 716 sheet: -2.68 (0.39), residues: 124 loop : -3.04 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 604 HIS 0.008 0.001 HIS A 102 PHE 0.037 0.002 PHE B 465 TYR 0.024 0.002 TYR B 225 ARG 0.003 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 THR cc_start: 0.9538 (OUTLIER) cc_final: 0.9243 (t) REVERT: A 186 GLU cc_start: 0.8994 (tt0) cc_final: 0.8771 (tp30) REVERT: A 253 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6815 (p0) REVERT: A 326 MET cc_start: 0.8634 (tpp) cc_final: 0.8425 (tpt) REVERT: A 333 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: A 347 MET cc_start: 0.8529 (mpp) cc_final: 0.8086 (mpp) REVERT: A 362 PHE cc_start: 0.8923 (t80) cc_final: 0.8596 (t80) REVERT: A 378 MET cc_start: 0.8352 (mpt) cc_final: 0.7709 (mpp) REVERT: A 413 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.8781 (tt) REVERT: A 548 ASP cc_start: 0.8999 (t0) cc_final: 0.8738 (m-30) REVERT: A 689 CYS cc_start: 0.9174 (m) cc_final: 0.8783 (m) REVERT: B 195 TYR cc_start: 0.9363 (m-80) cc_final: 0.8763 (m-80) REVERT: B 399 THR cc_start: 0.8408 (m) cc_final: 0.8116 (t) REVERT: B 441 PHE cc_start: 0.9205 (m-80) cc_final: 0.8967 (m-80) REVERT: B 456 PHE cc_start: 0.9099 (t80) cc_final: 0.8887 (t80) REVERT: B 463 HIS cc_start: 0.8900 (m90) cc_final: 0.8272 (m-70) REVERT: B 466 TYR cc_start: 0.7979 (m-10) cc_final: 0.7560 (m-10) REVERT: C 43 LEU cc_start: 0.9549 (mt) cc_final: 0.9318 (mt) REVERT: C 83 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8321 (mm-40) REVERT: C 93 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9057 (tt) REVERT: C 112 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8068 (tp) REVERT: C 163 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9131 (tp) REVERT: C 210 TYR cc_start: 0.8855 (m-80) cc_final: 0.8645 (m-80) REVERT: D 10 GLU cc_start: 0.9039 (tp30) cc_final: 0.8795 (tp30) outliers start: 75 outliers final: 48 residues processed: 234 average time/residue: 0.1707 time to fit residues: 61.2078 Evaluate side-chains 228 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 640 TRP Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055426 restraints weight = 49345.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056949 restraints weight = 28133.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058072 restraints weight = 18785.611| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10028 Z= 0.271 Angle : 0.779 13.156 13675 Z= 0.386 Chirality : 0.044 0.303 1584 Planarity : 0.005 0.061 1706 Dihedral : 6.773 57.975 1360 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.29 % Favored : 91.98 % Rotamer: Outliers : 5.83 % Allowed : 27.22 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1235 helix: 1.67 (0.19), residues: 716 sheet: -2.58 (0.39), residues: 124 loop : -2.93 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 174 HIS 0.006 0.001 HIS C 58 PHE 0.036 0.002 PHE B 465 TYR 0.022 0.002 TYR B 389 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8931 (tpp) cc_final: 0.8710 (mmp) REVERT: A 237 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: A 253 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6843 (p0) REVERT: A 347 MET cc_start: 0.8770 (mpp) cc_final: 0.8365 (mpp) REVERT: A 362 PHE cc_start: 0.8848 (t80) cc_final: 0.8585 (t80) REVERT: A 378 MET cc_start: 0.8222 (mpt) cc_final: 0.7587 (mpp) REVERT: A 413 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 689 CYS cc_start: 0.9136 (m) cc_final: 0.8695 (m) REVERT: B 181 TYR cc_start: 0.9146 (t80) cc_final: 0.8939 (t80) REVERT: B 195 TYR cc_start: 0.9422 (m-80) cc_final: 0.8927 (m-80) REVERT: B 399 THR cc_start: 0.8344 (m) cc_final: 0.7981 (t) REVERT: B 456 PHE cc_start: 0.8954 (t80) cc_final: 0.8701 (t80) REVERT: B 458 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: B 459 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8178 (tp40) REVERT: C 43 LEU cc_start: 0.9587 (mt) cc_final: 0.9370 (mt) REVERT: C 83 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8402 (mm-40) REVERT: C 93 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8851 (tt) REVERT: C 112 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8160 (tp) REVERT: C 218 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7687 (m-10) REVERT: D 10 GLU cc_start: 0.8962 (tp30) cc_final: 0.8711 (tp30) outliers start: 61 outliers final: 43 residues processed: 220 average time/residue: 0.1754 time to fit residues: 59.0848 Evaluate side-chains 219 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 GLU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055618 restraints weight = 50126.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057204 restraints weight = 28465.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058276 restraints weight = 18774.461| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10028 Z= 0.262 Angle : 0.776 13.012 13675 Z= 0.384 Chirality : 0.044 0.299 1584 Planarity : 0.005 0.060 1706 Dihedral : 6.243 56.332 1356 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.02 % Favored : 91.34 % Rotamer: Outliers : 6.30 % Allowed : 27.41 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1235 helix: 1.65 (0.19), residues: 715 sheet: -2.40 (0.40), residues: 124 loop : -2.95 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 174 HIS 0.006 0.001 HIS C 58 PHE 0.034 0.002 PHE B 465 TYR 0.021 0.002 TYR B 225 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6935 (p0) REVERT: A 343 MET cc_start: 0.8728 (tpt) cc_final: 0.8165 (tpt) REVERT: A 347 MET cc_start: 0.8800 (mpp) cc_final: 0.8022 (mpp) REVERT: A 689 CYS cc_start: 0.9148 (m) cc_final: 0.8695 (m) REVERT: B 181 TYR cc_start: 0.9150 (t80) cc_final: 0.8913 (t80) REVERT: B 195 TYR cc_start: 0.9432 (m-80) cc_final: 0.8963 (m-80) REVERT: B 210 MET cc_start: 0.8264 (mmm) cc_final: 0.7757 (mmt) REVERT: B 399 THR cc_start: 0.8267 (m) cc_final: 0.7910 (t) REVERT: B 441 PHE cc_start: 0.9214 (m-80) cc_final: 0.8906 (m-80) REVERT: B 450 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: B 456 PHE cc_start: 0.8970 (t80) cc_final: 0.8762 (t80) REVERT: B 457 MET cc_start: 0.8162 (mtm) cc_final: 0.7828 (mtm) REVERT: B 458 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8197 (m-30) REVERT: B 459 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7692 (tp40) REVERT: B 463 HIS cc_start: 0.8849 (m90) cc_final: 0.7693 (m-70) REVERT: C 72 LEU cc_start: 0.9015 (mt) cc_final: 0.8634 (mt) REVERT: C 83 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8470 (mm-40) REVERT: C 93 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8843 (tt) REVERT: C 112 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8109 (tp) REVERT: C 142 LEU cc_start: 0.9167 (mt) cc_final: 0.8945 (mt) REVERT: C 218 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: D 10 GLU cc_start: 0.8955 (tp30) cc_final: 0.8669 (tp30) outliers start: 66 outliers final: 50 residues processed: 214 average time/residue: 0.1653 time to fit residues: 54.4277 Evaluate side-chains 225 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 115 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055520 restraints weight = 50283.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057101 restraints weight = 28757.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.058194 restraints weight = 19014.782| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10028 Z= 0.285 Angle : 0.790 13.017 13675 Z= 0.392 Chirality : 0.045 0.300 1584 Planarity : 0.005 0.060 1706 Dihedral : 6.127 51.934 1356 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.26 % Favored : 91.09 % Rotamer: Outliers : 6.21 % Allowed : 27.60 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1235 helix: 1.61 (0.19), residues: 717 sheet: -2.33 (0.41), residues: 124 loop : -2.88 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 174 HIS 0.006 0.001 HIS C 58 PHE 0.044 0.002 PHE C 132 TYR 0.016 0.001 TYR A 569 ARG 0.003 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9038 (mm) REVERT: A 195 CYS cc_start: 0.4892 (m) cc_final: 0.4685 (m) REVERT: A 221 MET cc_start: 0.8365 (mmp) cc_final: 0.7354 (mmt) REVERT: A 253 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6989 (p0) REVERT: A 343 MET cc_start: 0.8856 (tpt) cc_final: 0.8241 (tpt) REVERT: A 347 MET cc_start: 0.8870 (mpp) cc_final: 0.8062 (mpp) REVERT: A 689 CYS cc_start: 0.9134 (m) cc_final: 0.8692 (m) REVERT: B 181 TYR cc_start: 0.9186 (t80) cc_final: 0.8977 (t80) REVERT: B 195 TYR cc_start: 0.9433 (m-80) cc_final: 0.8954 (m-80) REVERT: B 210 MET cc_start: 0.8411 (mmm) cc_final: 0.7852 (mmt) REVERT: B 399 THR cc_start: 0.8296 (m) cc_final: 0.7946 (t) REVERT: B 441 PHE cc_start: 0.9314 (m-80) cc_final: 0.8975 (m-80) REVERT: B 450 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8389 (m-30) REVERT: B 456 PHE cc_start: 0.9096 (t80) cc_final: 0.8890 (t80) REVERT: B 457 MET cc_start: 0.8099 (mtm) cc_final: 0.7858 (mtm) REVERT: B 458 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8389 (m-30) REVERT: B 459 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7794 (tp40) REVERT: B 463 HIS cc_start: 0.8912 (m90) cc_final: 0.7835 (m-70) REVERT: C 72 LEU cc_start: 0.9037 (mt) cc_final: 0.8656 (mt) REVERT: C 83 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8685 (mm-40) REVERT: C 93 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8868 (tt) REVERT: C 112 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8084 (tp) REVERT: C 218 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: D 10 GLU cc_start: 0.8972 (tp30) cc_final: 0.8758 (tp30) outliers start: 65 outliers final: 48 residues processed: 216 average time/residue: 0.1651 time to fit residues: 54.2562 Evaluate side-chains 220 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057144 restraints weight = 49139.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058805 restraints weight = 27648.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059795 restraints weight = 18040.084| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10028 Z= 0.213 Angle : 0.788 13.346 13675 Z= 0.383 Chirality : 0.045 0.293 1584 Planarity : 0.005 0.061 1706 Dihedral : 5.923 47.575 1356 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.53 % Favored : 91.82 % Rotamer: Outliers : 4.78 % Allowed : 29.51 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1235 helix: 1.55 (0.19), residues: 720 sheet: -2.25 (0.41), residues: 125 loop : -2.73 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP C 174 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.016 0.001 TYR B 225 ARG 0.003 0.000 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8329 (mmp) cc_final: 0.7291 (mmt) REVERT: A 253 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6848 (p0) REVERT: A 343 MET cc_start: 0.8882 (tpt) cc_final: 0.8579 (tpt) REVERT: A 347 MET cc_start: 0.8799 (mpp) cc_final: 0.8398 (mmp) REVERT: A 378 MET cc_start: 0.8480 (mpp) cc_final: 0.8277 (mpp) REVERT: A 689 CYS cc_start: 0.9101 (m) cc_final: 0.8673 (m) REVERT: B 195 TYR cc_start: 0.9439 (m-80) cc_final: 0.8962 (m-80) REVERT: B 210 MET cc_start: 0.8512 (mmm) cc_final: 0.7985 (mmt) REVERT: B 399 THR cc_start: 0.8200 (m) cc_final: 0.7824 (t) REVERT: B 456 PHE cc_start: 0.9099 (t80) cc_final: 0.8672 (t80) REVERT: B 458 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: B 463 HIS cc_start: 0.8946 (m90) cc_final: 0.8476 (m90) REVERT: C 41 PHE cc_start: 0.9062 (m-80) cc_final: 0.8838 (m-10) REVERT: C 72 LEU cc_start: 0.9046 (mt) cc_final: 0.8822 (mt) REVERT: C 83 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8684 (mm-40) REVERT: C 112 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8137 (tp) REVERT: C 142 LEU cc_start: 0.9029 (mt) cc_final: 0.8819 (mt) REVERT: C 218 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8012 (m-10) REVERT: D 20 LEU cc_start: 0.8564 (mt) cc_final: 0.8364 (pp) outliers start: 50 outliers final: 37 residues processed: 217 average time/residue: 0.1790 time to fit residues: 58.6099 Evaluate side-chains 213 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 6 optimal weight: 0.0670 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.055694 restraints weight = 50763.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057286 restraints weight = 29043.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058395 restraints weight = 19086.885| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10028 Z= 0.317 Angle : 0.825 12.669 13675 Z= 0.411 Chirality : 0.045 0.305 1584 Planarity : 0.005 0.074 1706 Dihedral : 5.703 46.529 1351 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.77 % Favored : 91.58 % Rotamer: Outliers : 4.87 % Allowed : 29.89 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1235 helix: 1.50 (0.19), residues: 718 sheet: -2.35 (0.42), residues: 117 loop : -2.62 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 174 HIS 0.006 0.001 HIS C 58 PHE 0.029 0.002 PHE B 465 TYR 0.018 0.002 TYR B 389 ARG 0.003 0.000 ARG A 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8403 (mmp) cc_final: 0.7399 (mmt) REVERT: A 343 MET cc_start: 0.8881 (tpt) cc_final: 0.8584 (tpt) REVERT: A 347 MET cc_start: 0.8776 (mpp) cc_final: 0.8424 (mmp) REVERT: A 689 CYS cc_start: 0.9132 (m) cc_final: 0.8686 (m) REVERT: B 195 TYR cc_start: 0.9433 (m-80) cc_final: 0.8954 (m-80) REVERT: B 210 MET cc_start: 0.8501 (mmm) cc_final: 0.7994 (mmt) REVERT: B 399 THR cc_start: 0.8325 (m) cc_final: 0.7964 (t) REVERT: B 441 PHE cc_start: 0.9153 (m-80) cc_final: 0.8841 (m-80) REVERT: B 450 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8437 (m-30) REVERT: B 458 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: B 463 HIS cc_start: 0.9079 (m90) cc_final: 0.8500 (m90) REVERT: C 35 LEU cc_start: 0.9507 (tp) cc_final: 0.9258 (tp) REVERT: C 72 LEU cc_start: 0.8816 (mt) cc_final: 0.8276 (mt) REVERT: C 83 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8704 (mm-40) REVERT: C 112 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8153 (tp) REVERT: C 218 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8004 (m-10) outliers start: 51 outliers final: 39 residues processed: 202 average time/residue: 0.1745 time to fit residues: 53.2288 Evaluate side-chains 211 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 83 optimal weight: 0.0040 chunk 111 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055122 restraints weight = 50358.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056724 restraints weight = 28508.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057827 restraints weight = 18611.199| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10028 Z= 0.330 Angle : 0.830 14.626 13675 Z= 0.410 Chirality : 0.045 0.307 1584 Planarity : 0.005 0.065 1706 Dihedral : 5.769 45.544 1351 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.42 % Favored : 90.93 % Rotamer: Outliers : 4.39 % Allowed : 30.75 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1235 helix: 1.31 (0.19), residues: 723 sheet: -2.14 (0.44), residues: 109 loop : -2.68 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP C 174 HIS 0.006 0.002 HIS A 553 PHE 0.029 0.002 PHE B 465 TYR 0.023 0.002 TYR B 225 ARG 0.004 0.000 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.40 seconds wall clock time: 50 minutes 0.10 seconds (3000.10 seconds total)