Starting phenix.real_space_refine on Wed Sep 17 16:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fn4_3239/09_2025/5fn4_3239.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fn4_3239/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/5fn4_3239/09_2025/5fn4_3239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fn4_3239/09_2025/5fn4_3239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5fn4_3239/09_2025/5fn4_3239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fn4_3239/09_2025/5fn4_3239.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.76, per 1000 atoms: 0.28 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: 1.04 Conformation dependent library (CDL) restraints added in 359.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.30 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: 1.66 Time building geometry restraints manager: 1.33 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: 0.540 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- 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 10033 Z= 0.663 Angle : 1.714 12.399 13685 Z= 1.235 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 371 TYR 0.043 0.004 TYR C 69 PHE 0.044 0.004 PHE B 176 TRP 0.031 0.003 TRP D 36 HIS 0.017 0.003 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00980 (10028) covalent geometry : angle 1.71310 (13675) SS BOND : bond 0.01344 ( 5) SS BOND : angle 2.28809 ( 10) hydrogen bonds : bond 0.14051 ( 594) hydrogen bonds : angle 5.73107 ( 1737) *********************** 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 : 0.387 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: 0.7921 (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: 0.8729 (ptm) REVERT: A 217 LEU cc_start: 0.8876 (tt) cc_final: 0.8544 (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: 0.9081 (mpp) REVERT: A 362 PHE cc_start: 0.8225 (t80) cc_final: 0.7953 (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: 0.8247 (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: 0.7799 (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: 0.8754 (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: 0.0880 time to fit residues: 47.9857 Evaluate side-chains 258 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0470 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 74 HIS A 417 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** A 531 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.069241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.058053 restraints weight = 48677.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059773 restraints weight = 27689.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060959 restraints weight = 18179.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061910 restraints weight = 13351.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.062328 restraints weight = 10447.040| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 0.046 10033 Z= 0.168 Angle : 0.839 11.024 13685 Z= 0.422 Chirality : 0.046 0.196 1584 Planarity : 0.006 0.061 1706 Dihedral : 9.877 66.022 1420 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 1.38 % Allowed : 8.18 % Favored : 90.45 % Rotamer: Outliers : 6.02 % Allowed : 21.01 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1235 helix: 2.66 (0.19), residues: 716 sheet: -3.18 (0.37), residues: 119 loop : -3.44 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 109 TYR 0.022 0.002 TYR A 565 PHE 0.031 0.002 PHE A 302 TRP 0.023 0.002 TRP D 36 HIS 0.012 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00364 (10028) covalent geometry : angle 0.83680 (13675) SS BOND : bond 0.00463 ( 5) SS BOND : angle 2.29433 ( 10) hydrogen bonds : bond 0.04472 ( 594) hydrogen bonds : angle 4.48604 ( 1737) *********************** 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 319 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 0.386 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: A 173 TYR cc_start: 0.3350 (t80) cc_final: 0.2844 (t80) REVERT: A 186 GLU cc_start: 0.9028 (tt0) cc_final: 0.8684 (tp30) REVERT: A 249 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: A 362 PHE cc_start: 0.8773 (t80) cc_final: 0.7554 (t80) REVERT: A 378 MET cc_start: 0.8075 (mpt) cc_final: 0.7370 (mpp) REVERT: A 413 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8788 (tt) REVERT: A 526 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.8998 (tp) REVERT: A 546 LEU cc_start: 0.9429 (mt) cc_final: 0.9210 (mt) REVERT: A 548 ASP cc_start: 0.9036 (t0) cc_final: 0.8804 (m-30) REVERT: B 168 ILE cc_start: 0.7503 (mm) cc_final: 0.7194 (mm) REVERT: B 184 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8968 (mm-30) REVERT: B 203 TRP cc_start: 0.9206 (t-100) cc_final: 0.8753 (t-100) REVERT: B 223 GLN cc_start: 0.8479 (mt0) cc_final: 0.7813 (mm-40) REVERT: B 244 TRP cc_start: 0.4972 (OUTLIER) cc_final: 0.4692 (m100) REVERT: B 441 PHE cc_start: 0.8773 (m-80) cc_final: 0.8472 (m-80) REVERT: B 458 ASP cc_start: 0.9050 (t0) cc_final: 0.8792 (m-30) REVERT: C 43 LEU cc_start: 0.9330 (mt) cc_final: 0.8964 (mt) REVERT: C 69 TYR cc_start: 0.8649 (t80) cc_final: 0.8433 (t80) REVERT: C 83 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8560 (mm-40) REVERT: C 93 LEU cc_start: 0.9251 (mt) cc_final: 0.8965 (tt) REVERT: C 127 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9237 (mp) REVERT: C 135 ILE cc_start: 0.9639 (tp) cc_final: 0.9268 (pt) REVERT: C 239 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8644 (tt) REVERT: D 20 LEU cc_start: 0.8360 (mt) cc_final: 0.8111 (pp) REVERT: D 38 PHE cc_start: 0.8524 (t80) cc_final: 0.8261 (t80) REVERT: D 62 VAL cc_start: 0.8588 (t) cc_final: 0.8349 (m) REVERT: D 76 THR cc_start: 0.8931 (m) cc_final: 0.8691 (p) outliers start: 63 outliers final: 29 residues processed: 298 average time/residue: 0.0747 time to fit residues: 33.3851 Evaluate side-chains 227 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 134 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 239 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 76 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 222 HIS A 305 GLN A 313 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 531 ASN A 535 GLN A 606 GLN B 190 ASN C 150 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.064679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054180 restraints weight = 50678.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055744 restraints weight = 28720.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056780 restraints weight = 18981.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057585 restraints weight = 14088.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058095 restraints weight = 11068.422| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 10033 Z= 0.316 Angle : 0.868 19.736 13685 Z= 0.445 Chirality : 0.047 0.292 1584 Planarity : 0.006 0.066 1706 Dihedral : 8.382 63.005 1378 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.74 % Favored : 90.28 % Rotamer: Outliers : 8.12 % Allowed : 20.44 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.24), residues: 1235 helix: 1.80 (0.19), residues: 719 sheet: -3.20 (0.36), residues: 124 loop : -3.32 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 371 TYR 0.026 0.002 TYR B 225 PHE 0.039 0.003 PHE B 465 TRP 0.032 0.002 TRP C 174 HIS 0.009 0.002 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00683 (10028) covalent geometry : angle 0.86126 (13675) SS BOND : bond 0.01626 ( 5) SS BOND : angle 3.97501 ( 10) hydrogen bonds : bond 0.04660 ( 594) hydrogen bonds : angle 4.79033 ( 1737) *********************** 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 277 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 192 time to evaluate : 0.281 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 95 MET cc_start: 0.8903 (mmm) cc_final: 0.8677 (mmm) REVERT: A 173 TYR cc_start: 0.2899 (t80) cc_final: 0.1815 (t80) REVERT: A 186 GLU cc_start: 0.8963 (tt0) cc_final: 0.8711 (tp30) REVERT: A 221 MET cc_start: 0.8994 (mmp) cc_final: 0.8217 (tpp) REVERT: A 362 PHE cc_start: 0.8905 (t80) cc_final: 0.8260 (t80) REVERT: A 378 MET cc_start: 0.8304 (mpt) cc_final: 0.7626 (mpp) REVERT: A 413 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8833 (tt) REVERT: A 526 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9395 (mm) REVERT: A 546 LEU cc_start: 0.9516 (mt) cc_final: 0.9248 (mt) REVERT: A 548 ASP cc_start: 0.9067 (t0) cc_final: 0.8697 (m-30) REVERT: B 203 TRP cc_start: 0.9029 (t-100) cc_final: 0.8793 (t-100) REVERT: B 223 GLN cc_start: 0.8391 (mt0) cc_final: 0.7764 (mm-40) REVERT: B 244 TRP cc_start: 0.5422 (OUTLIER) cc_final: 0.4983 (m100) REVERT: B 399 THR cc_start: 0.8344 (m) cc_final: 0.8074 (t) REVERT: B 441 PHE cc_start: 0.9013 (m-80) cc_final: 0.8676 (m-80) REVERT: B 458 ASP cc_start: 0.8941 (t0) cc_final: 0.8673 (m-30) REVERT: C 43 LEU cc_start: 0.9475 (mt) cc_final: 0.9215 (mt) REVERT: C 83 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8506 (mm-40) REVERT: C 135 ILE cc_start: 0.9661 (tp) cc_final: 0.9230 (pt) REVERT: C 138 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9409 (mt) REVERT: D 62 VAL cc_start: 0.8648 (t) cc_final: 0.8443 (m) outliers start: 85 outliers final: 56 residues processed: 247 average time/residue: 0.0709 time to fit residues: 26.5573 Evaluate side-chains 240 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 441 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 660 ILE 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 176 PHE 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 412 VAL 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 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 19 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 220 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.067219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.056593 restraints weight = 49232.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058203 restraints weight = 27624.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059284 restraints weight = 18105.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060095 restraints weight = 13295.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060543 restraints weight = 10408.564| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10033 Z= 0.151 Angle : 0.774 11.580 13685 Z= 0.379 Chirality : 0.044 0.296 1584 Planarity : 0.005 0.062 1706 Dihedral : 7.446 57.264 1364 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.80 % Favored : 92.31 % Rotamer: Outliers : 5.54 % Allowed : 23.50 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.25), residues: 1235 helix: 1.94 (0.19), residues: 710 sheet: -2.65 (0.39), residues: 126 loop : -2.94 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 31 TYR 0.031 0.002 TYR D 56 PHE 0.038 0.002 PHE B 465 TRP 0.024 0.002 TRP A 604 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00336 (10028) covalent geometry : angle 0.77101 (13675) SS BOND : bond 0.00691 ( 5) SS BOND : angle 2.46514 ( 10) hydrogen bonds : bond 0.04046 ( 594) hydrogen bonds : angle 4.43298 ( 1737) *********************** 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 263 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9266 (t) REVERT: A 162 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.7018 (pt) REVERT: A 173 TYR cc_start: 0.2450 (t80) cc_final: 0.1152 (t80) REVERT: A 186 GLU cc_start: 0.8887 (tt0) cc_final: 0.8681 (tp30) REVERT: A 221 MET cc_start: 0.8924 (mmp) cc_final: 0.8207 (tpp) REVERT: A 378 MET cc_start: 0.8287 (mpt) cc_final: 0.8045 (mpp) REVERT: A 548 ASP cc_start: 0.8879 (t0) cc_final: 0.8596 (m-30) REVERT: A 689 CYS cc_start: 0.9117 (m) cc_final: 0.8739 (m) REVERT: B 181 TYR cc_start: 0.9368 (t80) cc_final: 0.9040 (t80) REVERT: B 223 GLN cc_start: 0.8395 (mt0) cc_final: 0.7700 (mm-40) REVERT: B 399 THR cc_start: 0.8269 (m) cc_final: 0.7918 (t) REVERT: B 441 PHE cc_start: 0.9054 (m-80) cc_final: 0.8769 (m-80) REVERT: B 453 VAL cc_start: 0.9309 (t) cc_final: 0.9022 (t) REVERT: B 457 MET cc_start: 0.8250 (ptt) cc_final: 0.7930 (ptt) REVERT: B 458 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8734 (m-30) REVERT: C 43 LEU cc_start: 0.9434 (mt) cc_final: 0.9201 (mt) REVERT: C 69 TYR cc_start: 0.8618 (t80) cc_final: 0.8345 (t80) REVERT: C 83 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8476 (mm-40) REVERT: C 93 LEU cc_start: 0.9115 (mt) cc_final: 0.8864 (tt) REVERT: C 112 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.8020 (tp) REVERT: C 135 ILE cc_start: 0.9618 (tp) cc_final: 0.9114 (pt) REVERT: D 38 PHE cc_start: 0.8425 (t80) cc_final: 0.8142 (t80) REVERT: D 76 THR cc_start: 0.8808 (m) cc_final: 0.8588 (p) outliers start: 58 outliers final: 33 residues processed: 244 average time/residue: 0.0691 time to fit residues: 26.3417 Evaluate side-chains 220 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 THR 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 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 604 TRP Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 LEU 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 412 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain C residue 20 LEU 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 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 10 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN B 190 ASN ** 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 = 0.066409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056069 restraints weight = 48954.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057681 restraints weight = 27769.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058759 restraints weight = 18048.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.059568 restraints weight = 13190.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060187 restraints weight = 10238.661| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10033 Z= 0.182 Angle : 0.762 11.641 13685 Z= 0.380 Chirality : 0.044 0.302 1584 Planarity : 0.005 0.059 1706 Dihedral : 7.013 58.785 1362 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.69 % Favored : 91.42 % Rotamer: Outliers : 6.11 % Allowed : 23.69 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.24), residues: 1235 helix: 1.82 (0.19), residues: 710 sheet: -2.52 (0.39), residues: 124 loop : -2.92 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 31 TYR 0.023 0.002 TYR D 56 PHE 0.035 0.002 PHE B 465 TRP 0.045 0.002 TRP C 174 HIS 0.010 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00410 (10028) covalent geometry : angle 0.75840 (13675) SS BOND : bond 0.00404 ( 5) SS BOND : angle 2.72898 ( 10) hydrogen bonds : bond 0.04025 ( 594) hydrogen bonds : angle 4.55046 ( 1737) *********************** 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 255 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.372 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: 0.3162 (t80) cc_final: 0.1526 (t80) REVERT: A 186 GLU cc_start: 0.8937 (tt0) cc_final: 0.8722 (tp30) REVERT: A 221 MET cc_start: 0.9004 (mmp) cc_final: 0.8565 (mmp) REVERT: A 237 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8954 (mt0) REVERT: A 253 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6765 (p0) REVERT: A 310 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: A 362 PHE cc_start: 0.8883 (t80) cc_final: 0.8505 (t80) REVERT: A 378 MET cc_start: 0.8322 (mpt) cc_final: 0.8042 (mpp) REVERT: A 548 ASP cc_start: 0.8973 (t0) cc_final: 0.8730 (m-30) REVERT: A 689 CYS cc_start: 0.9181 (m) cc_final: 0.8829 (m) REVERT: B 181 TYR cc_start: 0.9289 (t80) cc_final: 0.9036 (t80) REVERT: B 195 TYR cc_start: 0.9362 (m-80) cc_final: 0.8636 (m-80) REVERT: B 223 GLN cc_start: 0.8424 (mt0) cc_final: 0.7727 (mm-40) REVERT: B 399 THR cc_start: 0.8261 (m) cc_final: 0.7938 (t) REVERT: B 441 PHE cc_start: 0.9134 (m-80) cc_final: 0.8885 (m-80) REVERT: B 463 HIS cc_start: 0.8909 (m90) cc_final: 0.8278 (m-70) REVERT: B 466 TYR cc_start: 0.8031 (m-10) cc_final: 0.7676 (m-10) REVERT: C 43 LEU cc_start: 0.9477 (mt) cc_final: 0.9230 (mt) REVERT: C 69 TYR cc_start: 0.8613 (t80) cc_final: 0.8331 (t80) REVERT: C 83 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8382 (mm-40) REVERT: C 93 LEU cc_start: 0.9156 (mt) cc_final: 0.8916 (tt) REVERT: C 112 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7985 (tp) REVERT: C 142 LEU cc_start: 0.9086 (mt) cc_final: 0.8841 (mt) REVERT: C 163 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9120 (tp) REVERT: D 18 TYR cc_start: 0.8352 (m-80) cc_final: 0.8103 (m-80) REVERT: D 38 PHE cc_start: 0.8461 (t80) cc_final: 0.8216 (t80) REVERT: D 76 THR cc_start: 0.8968 (m) cc_final: 0.8737 (p) outliers start: 64 outliers final: 45 residues processed: 232 average time/residue: 0.0692 time to fit residues: 25.0650 Evaluate side-chains 228 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 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 310 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 436 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 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 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 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 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 83 GLN Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 127 ILE 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 53 ILE 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 117 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.0050 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 0.0670 overall best weight: 0.5734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN 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 = 0.3394 r_free = 0.3394 target = 0.068653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058383 restraints weight = 47268.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060017 restraints weight = 27039.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061106 restraints weight = 17657.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061892 restraints weight = 12843.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062525 restraints weight = 10064.963| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10033 Z= 0.135 Angle : 0.766 12.814 13685 Z= 0.370 Chirality : 0.044 0.293 1584 Planarity : 0.005 0.059 1706 Dihedral : 6.665 59.522 1360 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.64 % Favored : 92.55 % Rotamer: Outliers : 4.68 % Allowed : 26.84 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.24), residues: 1235 helix: 1.79 (0.19), residues: 714 sheet: -2.32 (0.40), residues: 125 loop : -2.85 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 31 TYR 0.025 0.001 TYR D 56 PHE 0.035 0.002 PHE B 465 TRP 0.035 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00297 (10028) covalent geometry : angle 0.76291 (13675) SS BOND : bond 0.00486 ( 5) SS BOND : angle 2.56966 ( 10) hydrogen bonds : bond 0.03868 ( 594) hydrogen bonds : angle 4.42165 ( 1737) *********************** 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 260 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8777 (mmp) cc_final: 0.8544 (mmp) REVERT: A 245 GLU cc_start: 0.8064 (pt0) cc_final: 0.7533 (pt0) REVERT: A 253 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6832 (p0) REVERT: A 305 GLN cc_start: 0.8525 (tt0) cc_final: 0.8264 (tt0) REVERT: A 362 PHE cc_start: 0.8881 (t80) cc_final: 0.8598 (t80) REVERT: A 378 MET cc_start: 0.8310 (mpt) cc_final: 0.8053 (mpp) REVERT: A 689 CYS cc_start: 0.9147 (m) cc_final: 0.8700 (m) REVERT: B 168 ILE cc_start: 0.6945 (mm) cc_final: 0.6701 (mp) REVERT: B 195 TYR cc_start: 0.9419 (m-80) cc_final: 0.8762 (m-80) REVERT: B 222 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 223 GLN cc_start: 0.8400 (mt0) cc_final: 0.7558 (mm-40) REVERT: B 389 TYR cc_start: 0.9078 (m-80) cc_final: 0.8798 (m-80) REVERT: B 399 THR cc_start: 0.8158 (m) cc_final: 0.7855 (t) REVERT: B 432 LEU cc_start: 0.6506 (mp) cc_final: 0.6206 (tt) REVERT: B 454 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8464 (tp40) REVERT: B 463 HIS cc_start: 0.8834 (m90) cc_final: 0.8384 (m90) REVERT: C 43 LEU cc_start: 0.9509 (mt) cc_final: 0.9282 (mt) REVERT: C 69 TYR cc_start: 0.8451 (t80) cc_final: 0.8180 (t80) REVERT: C 83 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8318 (mm-40) REVERT: C 95 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8453 (mmmt) REVERT: C 119 TYR cc_start: 0.8814 (t80) cc_final: 0.8313 (t80) REVERT: C 192 LEU cc_start: 0.8944 (mt) cc_final: 0.8730 (tt) REVERT: C 210 TYR cc_start: 0.8635 (m-80) cc_final: 0.8093 (m-80) REVERT: C 211 GLU cc_start: 0.8489 (mp0) cc_final: 0.8280 (mp0) REVERT: C 218 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7784 (m-10) REVERT: D 18 TYR cc_start: 0.8103 (m-80) cc_final: 0.7766 (m-80) REVERT: D 38 PHE cc_start: 0.8262 (t80) cc_final: 0.8012 (t80) REVERT: D 73 SER cc_start: 0.8965 (m) cc_final: 0.8592 (p) REVERT: D 76 THR cc_start: 0.8953 (m) cc_final: 0.8707 (p) outliers start: 49 outliers final: 24 residues processed: 242 average time/residue: 0.0671 time to fit residues: 24.9870 Evaluate side-chains 212 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 LEU 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 312 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 565 TYR 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 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 454 GLN Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 88 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN ** 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 = 0.3328 r_free = 0.3328 target = 0.065273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055226 restraints weight = 49231.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056755 restraints weight = 27797.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.057846 restraints weight = 18339.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.058647 restraints weight = 13285.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059146 restraints weight = 10332.497| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10033 Z= 0.258 Angle : 0.804 14.350 13685 Z= 0.412 Chirality : 0.045 0.311 1584 Planarity : 0.006 0.072 1706 Dihedral : 6.164 56.749 1353 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.94 % Favored : 91.34 % Rotamer: Outliers : 5.73 % Allowed : 26.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.24), residues: 1235 helix: 1.54 (0.19), residues: 711 sheet: -2.43 (0.39), residues: 124 loop : -2.71 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 82 TYR 0.029 0.002 TYR B 181 PHE 0.031 0.002 PHE B 465 TRP 0.067 0.003 TRP C 174 HIS 0.008 0.002 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00560 (10028) covalent geometry : angle 0.79966 (13675) SS BOND : bond 0.01052 ( 5) SS BOND : angle 3.13553 ( 10) hydrogen bonds : bond 0.04246 ( 594) hydrogen bonds : angle 4.76030 ( 1737) *********************** 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 238 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7150 (p0) REVERT: A 378 MET cc_start: 0.8363 (mpt) cc_final: 0.8118 (mpp) REVERT: A 689 CYS cc_start: 0.9209 (m) cc_final: 0.8853 (m) REVERT: B 195 TYR cc_start: 0.9393 (m-80) cc_final: 0.8931 (m-80) REVERT: B 210 MET cc_start: 0.8398 (mmm) cc_final: 0.7795 (mmt) REVERT: B 222 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 223 GLN cc_start: 0.8332 (mt0) cc_final: 0.7589 (mm-40) REVERT: B 399 THR cc_start: 0.8350 (m) cc_final: 0.8025 (t) REVERT: B 441 PHE cc_start: 0.9231 (m-80) cc_final: 0.8929 (m-80) REVERT: B 463 HIS cc_start: 0.8982 (m90) cc_final: 0.8367 (m90) REVERT: C 83 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8358 (mm-40) REVERT: C 117 MET cc_start: 0.8444 (ptp) cc_final: 0.8236 (ptp) REVERT: C 218 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7998 (m-10) REVERT: C 224 MET cc_start: 0.9250 (mmp) cc_final: 0.9028 (mmp) REVERT: D 10 GLU cc_start: 0.8992 (tp30) cc_final: 0.8730 (tp30) REVERT: D 62 VAL cc_start: 0.8669 (t) cc_final: 0.8469 (m) REVERT: D 76 THR cc_start: 0.9056 (m) cc_final: 0.8817 (t) outliers start: 60 outliers final: 46 residues processed: 212 average time/residue: 0.0713 time to fit residues: 23.5861 Evaluate side-chains 218 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 325 VAL 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 526 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 565 TYR 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 697 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ILE 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 388 PHE Chi-restraints excluded: chain B residue 392 LEU 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 7 PHE 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 86 PHE Chi-restraints excluded: chain C residue 112 ILE 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 32 VAL Chi-restraints excluded: chain D residue 53 ILE 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 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057004 restraints weight = 49051.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058614 restraints weight = 27801.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059699 restraints weight = 18224.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060510 restraints weight = 13293.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061130 restraints weight = 10478.244| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10033 Z= 0.151 Angle : 0.788 13.068 13685 Z= 0.384 Chirality : 0.045 0.295 1584 Planarity : 0.005 0.060 1706 Dihedral : 5.915 49.627 1353 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.53 % Favored : 91.74 % Rotamer: Outliers : 4.58 % Allowed : 27.22 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1235 helix: 1.61 (0.19), residues: 711 sheet: -2.34 (0.39), residues: 124 loop : -2.63 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 82 TYR 0.015 0.001 TYR A 569 PHE 0.040 0.002 PHE C 132 TRP 0.053 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00336 (10028) covalent geometry : angle 0.78579 (13675) SS BOND : bond 0.00471 ( 5) SS BOND : angle 2.07781 ( 10) hydrogen bonds : bond 0.03998 ( 594) hydrogen bonds : angle 4.59959 ( 1737) *********************** 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 239 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9155 (mt) REVERT: A 237 GLN cc_start: 0.8878 (mt0) cc_final: 0.8449 (pt0) REVERT: A 253 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6879 (p0) REVERT: A 378 MET cc_start: 0.8329 (mpt) cc_final: 0.8103 (mpp) REVERT: A 689 CYS cc_start: 0.9177 (m) cc_final: 0.8817 (m) REVERT: B 84 MET cc_start: 0.8898 (ptt) cc_final: 0.8517 (ppp) REVERT: B 195 TYR cc_start: 0.9427 (m-80) cc_final: 0.9023 (m-80) REVERT: B 210 MET cc_start: 0.8505 (mmm) cc_final: 0.7845 (mmt) REVERT: B 222 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 223 GLN cc_start: 0.8367 (mt0) cc_final: 0.7520 (mm-40) REVERT: B 399 THR cc_start: 0.8245 (m) cc_final: 0.7878 (t) REVERT: B 432 LEU cc_start: 0.6552 (mp) cc_final: 0.6213 (tt) REVERT: B 441 PHE cc_start: 0.9265 (m-80) cc_final: 0.8922 (m-80) REVERT: B 450 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8448 (m-30) REVERT: B 458 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: B 463 HIS cc_start: 0.8979 (m90) cc_final: 0.8377 (m90) REVERT: C 83 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8432 (mm-40) REVERT: C 218 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8025 (m-10) REVERT: D 76 THR cc_start: 0.9033 (m) cc_final: 0.8782 (t) outliers start: 48 outliers final: 35 residues processed: 219 average time/residue: 0.0681 time to fit residues: 23.2885 Evaluate side-chains 210 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 325 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 565 TYR 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 B residue 80 LYS 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 383 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 458 ASP 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 83 GLN Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 112 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 53 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3392 r_free = 0.3392 target = 0.068216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.057889 restraints weight = 47911.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059515 restraints weight = 27022.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.060587 restraints weight = 17688.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.061438 restraints weight = 12988.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061976 restraints weight = 10058.131| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10033 Z= 0.149 Angle : 0.817 13.443 13685 Z= 0.399 Chirality : 0.045 0.301 1584 Planarity : 0.005 0.060 1706 Dihedral : 5.698 47.488 1351 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.61 % Favored : 91.66 % Rotamer: Outliers : 4.39 % Allowed : 28.84 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.24), residues: 1235 helix: 1.44 (0.19), residues: 716 sheet: -1.93 (0.41), residues: 115 loop : -2.67 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 82 TYR 0.017 0.001 TYR B 225 PHE 0.032 0.002 PHE B 465 TRP 0.083 0.002 TRP C 174 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00335 (10028) covalent geometry : angle 0.81398 (13675) SS BOND : bond 0.00623 ( 5) SS BOND : angle 2.55278 ( 10) hydrogen bonds : bond 0.04017 ( 594) hydrogen bonds : angle 4.66859 ( 1737) *********************** 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 224 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8873 (mmm) cc_final: 0.8299 (mmm) REVERT: A 237 GLN cc_start: 0.8877 (mt0) cc_final: 0.8569 (pt0) REVERT: A 253 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6870 (p0) REVERT: A 362 PHE cc_start: 0.8859 (t80) cc_final: 0.8607 (t80) REVERT: A 378 MET cc_start: 0.8356 (mpt) cc_final: 0.8139 (mpp) REVERT: A 689 CYS cc_start: 0.9189 (m) cc_final: 0.8837 (m) REVERT: B 84 MET cc_start: 0.8862 (ptt) cc_final: 0.8490 (ppp) REVERT: B 101 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8126 (tmtt) REVERT: B 195 TYR cc_start: 0.9427 (m-80) cc_final: 0.9079 (m-80) REVERT: B 222 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 223 GLN cc_start: 0.8347 (mt0) cc_final: 0.7504 (mm-40) REVERT: B 399 THR cc_start: 0.8055 (m) cc_final: 0.7707 (t) REVERT: B 432 LEU cc_start: 0.6508 (mp) cc_final: 0.6187 (tt) REVERT: B 441 PHE cc_start: 0.9273 (m-80) cc_final: 0.8884 (m-80) REVERT: B 454 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7507 (tp40) REVERT: B 458 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: B 463 HIS cc_start: 0.8971 (m90) cc_final: 0.8410 (m90) REVERT: C 22 LEU cc_start: 0.9450 (mm) cc_final: 0.9214 (mm) REVERT: C 72 LEU cc_start: 0.8803 (mt) cc_final: 0.8519 (mt) REVERT: C 83 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8478 (mm-40) REVERT: C 218 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7968 (m-10) REVERT: D 76 THR cc_start: 0.8991 (m) cc_final: 0.8747 (t) outliers start: 46 outliers final: 35 residues processed: 205 average time/residue: 0.0666 time to fit residues: 21.4407 Evaluate side-chains 214 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 VAL 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 526 LEU Chi-restraints excluded: chain A residue 565 TYR 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 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 420 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 458 ASP 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 83 GLN Chi-restraints excluded: chain C residue 112 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 53 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3391 r_free = 0.3391 target = 0.068128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058002 restraints weight = 47892.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059614 restraints weight = 27162.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.060705 restraints weight = 17696.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061411 restraints weight = 12832.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062097 restraints weight = 10131.057| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10033 Z= 0.160 Angle : 0.823 13.267 13685 Z= 0.404 Chirality : 0.046 0.298 1584 Planarity : 0.005 0.059 1706 Dihedral : 5.541 46.738 1349 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.61 % Favored : 91.66 % Rotamer: Outliers : 4.30 % Allowed : 29.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.24), residues: 1235 helix: 1.46 (0.19), residues: 709 sheet: -1.92 (0.42), residues: 115 loop : -2.58 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 82 TYR 0.017 0.001 TYR D 56 PHE 0.029 0.002 PHE B 465 TRP 0.070 0.002 TRP C 174 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00362 (10028) covalent geometry : angle 0.81965 (13675) SS BOND : bond 0.00634 ( 5) SS BOND : angle 2.83658 ( 10) hydrogen bonds : bond 0.04079 ( 594) hydrogen bonds : angle 4.63517 ( 1737) ********************** 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: 45 poor density : 177 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8896 (mmm) cc_final: 0.8307 (mmm) REVERT: A 237 GLN cc_start: 0.8901 (mt0) cc_final: 0.8657 (pt0) REVERT: A 253 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6806 (p0) REVERT: A 362 PHE cc_start: 0.8901 (t80) cc_final: 0.8477 (t80) REVERT: A 689 CYS cc_start: 0.9197 (m) cc_final: 0.8841 (m) REVERT: B 84 MET cc_start: 0.8898 (ptt) cc_final: 0.8519 (ppp) REVERT: B 101 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8189 (tmtt) REVERT: B 184 GLU cc_start: 0.8972 (tp30) cc_final: 0.8454 (tm-30) REVERT: B 195 TYR cc_start: 0.9429 (m-80) cc_final: 0.9086 (m-80) REVERT: B 210 MET cc_start: 0.8455 (mmm) cc_final: 0.8054 (mmt) REVERT: B 222 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 223 GLN cc_start: 0.8345 (mt0) cc_final: 0.8013 (pt0) REVERT: B 399 THR cc_start: 0.8005 (m) cc_final: 0.7670 (t) REVERT: B 432 LEU cc_start: 0.6460 (mp) cc_final: 0.6130 (tt) REVERT: B 441 PHE cc_start: 0.9256 (m-80) cc_final: 0.8869 (m-80) REVERT: B 458 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: B 463 HIS cc_start: 0.8969 (m90) cc_final: 0.8444 (m90) REVERT: C 72 LEU cc_start: 0.8735 (mt) cc_final: 0.8491 (mt) REVERT: C 83 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8579 (mm-40) REVERT: C 218 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: D 76 THR cc_start: 0.9008 (m) cc_final: 0.8771 (t) outliers start: 45 outliers final: 39 residues processed: 203 average time/residue: 0.0691 time to fit residues: 22.0390 Evaluate side-chains 215 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 253 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 VAL 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 519 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 565 TYR 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 686 VAL 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 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 23 ILE 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 137 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 9 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 454 GLN ** B 459 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 = 0.3381 r_free = 0.3381 target = 0.067524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057254 restraints weight = 48071.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.058887 restraints weight = 27135.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.059958 restraints weight = 17669.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060755 restraints weight = 12893.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061419 restraints weight = 9951.752| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10033 Z= 0.173 Angle : 0.808 13.048 13685 Z= 0.398 Chirality : 0.045 0.298 1584 Planarity : 0.005 0.060 1706 Dihedral : 5.531 45.846 1349 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.77 % Favored : 91.50 % Rotamer: Outliers : 4.49 % Allowed : 29.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.24), residues: 1235 helix: 1.32 (0.19), residues: 715 sheet: -1.94 (0.44), residues: 108 loop : -2.52 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 82 TYR 0.018 0.002 TYR B 225 PHE 0.028 0.002 PHE B 465 TRP 0.069 0.002 TRP C 174 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00388 (10028) covalent geometry : angle 0.80635 (13675) SS BOND : bond 0.00560 ( 5) SS BOND : angle 2.15571 ( 10) hydrogen bonds : bond 0.04110 ( 594) hydrogen bonds : angle 4.66630 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1468.18 seconds wall clock time: 26 minutes 16.67 seconds (1576.67 seconds total)