Starting phenix.real_space_refine on Fri Dec 27 14:54:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wh8_32497/12_2024/7wh8_32497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wh8_32497/12_2024/7wh8_32497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wh8_32497/12_2024/7wh8_32497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wh8_32497/12_2024/7wh8_32497.map" model { file = "/net/cci-nas-00/data/ceres_data/7wh8_32497/12_2024/7wh8_32497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wh8_32497/12_2024/7wh8_32497.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 23 5.16 5 C 3462 2.51 5 N 924 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5479 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "C" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2190 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 16, 'TRANS': 260} Time building chain proxies: 4.54, per 1000 atoms: 0.83 Number of scatterers: 5479 At special positions: 0 Unit cell: (74.6572, 83.4404, 161.391, 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 23 16.00 O 1070 8.00 N 924 7.00 C 3462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " 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: 1.21 Conformation dependent library (CDL) restraints added in 628.8 milliseconds 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 6.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.024A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.139A pdb=" N PHE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.351A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.984A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.762A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.761A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.967A pdb=" N VAL B 110 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 73 Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.531A pdb=" N LYS B 151 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 148 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 132 removed outlier: 3.531A pdb=" N LYS B 151 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 148 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 158 through 162 removed outlier: 3.534A pdb=" N SER B 161 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 217 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 215 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.689A pdb=" N CYS A 23 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE A 71 " --> pdb=" O CYS A 23 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.495A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 118 removed outlier: 6.018A pdb=" N TYR A 173 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 154 through 155 removed outlier: 4.437A pdb=" N TRP A 148 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 328 removed outlier: 4.104A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.536A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.055A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 474 181 hydrogen bonds defined for protein. 441 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: 1.80 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1766 1.34 - 1.46: 1286 1.46 - 1.58: 2530 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 5608 Sorted by residual: bond pdb=" N LEU B 101 " pdb=" CA LEU B 101 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.81e+00 bond pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.34e-02 5.57e+03 5.33e+00 bond pdb=" C VAL A 29 " pdb=" O VAL A 29 " ideal model delta sigma weight residual 1.238 1.221 0.016 1.06e-02 8.90e+03 2.32e+00 bond pdb=" N TYR A 32 " pdb=" CA TYR A 32 " ideal model delta sigma weight residual 1.462 1.445 0.016 1.26e-02 6.30e+03 1.70e+00 bond pdb=" C GLN C 493 " pdb=" O GLN C 493 " ideal model delta sigma weight residual 1.234 1.219 0.015 1.22e-02 6.72e+03 1.51e+00 ... (remaining 5603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 7487 2.31 - 4.62: 126 4.62 - 6.93: 10 6.93 - 9.24: 1 9.24 - 11.55: 1 Bond angle restraints: 7625 Sorted by residual: angle pdb=" N LEU B 101 " pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 110.80 122.35 -11.55 2.13e+00 2.20e-01 2.94e+01 angle pdb=" N PHE B 103 " pdb=" CA PHE B 103 " pdb=" C PHE B 103 " ideal model delta sigma weight residual 113.20 119.10 -5.90 1.21e+00 6.83e-01 2.38e+01 angle pdb=" N ASN A 93 " pdb=" CA ASN A 93 " pdb=" C ASN A 93 " ideal model delta sigma weight residual 108.79 113.62 -4.83 1.53e+00 4.27e-01 9.96e+00 angle pdb=" N VAL B 119 " pdb=" CA VAL B 119 " pdb=" C VAL B 119 " ideal model delta sigma weight residual 107.28 112.05 -4.77 1.59e+00 3.96e-01 9.01e+00 angle pdb=" N TYR B 106 " pdb=" CA TYR B 106 " pdb=" C TYR B 106 " ideal model delta sigma weight residual 111.02 114.57 -3.55 1.22e+00 6.72e-01 8.48e+00 ... (remaining 7620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 2995 17.35 - 34.69: 278 34.69 - 52.04: 63 52.04 - 69.39: 11 69.39 - 86.74: 8 Dihedral angle restraints: 3355 sinusoidal: 1298 harmonic: 2057 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 165.74 -72.74 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS B 148 " pdb=" SG CYS B 148 " pdb=" SG CYS B 204 " pdb=" CB CYS B 204 " ideal model delta sinusoidal sigma weight residual 93.00 157.22 -64.22 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -33.22 -52.78 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 3352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 784 0.092 - 0.184: 62 0.184 - 0.276: 1 0.276 - 0.368: 0 0.368 - 0.461: 2 Chirality restraints: 849 Sorted by residual: chirality pdb=" CA PHE B 103 " pdb=" N PHE B 103 " pdb=" C PHE B 103 " pdb=" CB PHE B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA LEU B 101 " pdb=" N LEU B 101 " pdb=" C LEU B 101 " pdb=" CB LEU B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA ASN A 93 " pdb=" N ASN A 93 " pdb=" C ASN A 93 " pdb=" CB ASN A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 846 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 220 " -0.059 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO B 221 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 209 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO B 210 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 100 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C GLY B 100 " 0.044 2.00e-02 2.50e+03 pdb=" O GLY B 100 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 101 " -0.015 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 890 2.77 - 3.30: 4954 3.30 - 3.83: 8526 3.83 - 4.37: 9987 4.37 - 4.90: 18117 Nonbonded interactions: 42474 Sorted by model distance: nonbonded pdb=" O SER A 28 " pdb=" OG SER A 28 " model vdw 2.233 3.040 nonbonded pdb=" CB LEU B 132 " pdb=" O GLY B 147 " model vdw 2.236 2.752 nonbonded pdb=" O ILE A 106 " pdb=" OH TYR A 140 " model vdw 2.273 3.040 nonbonded pdb=" O LEU A 13 " pdb=" N LYS A 107 " model vdw 2.288 3.120 nonbonded pdb=" O SER B 223 " pdb=" OG SER B 223 " model vdw 2.299 3.040 ... (remaining 42469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.370 Find NCS groups from input model: 0.060 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.004 0.057 5608 Z= 0.234 Angle : 0.709 11.555 7625 Z= 0.398 Chirality : 0.051 0.461 849 Planarity : 0.005 0.088 990 Dihedral : 14.335 86.735 2014 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.60 % Favored : 90.97 % Rotamer: Outliers : 2.61 % Allowed : 1.63 % Favored : 95.75 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.32), residues: 709 helix: -2.17 (0.88), residues: 35 sheet: -1.35 (0.36), residues: 228 loop : -1.42 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.002 0.001 HIS A 198 PHE 0.014 0.001 PHE C 377 TYR 0.014 0.001 TYR C 495 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.675 Fit side-chains REVERT: B 81 MET cc_start: 0.8857 (tmm) cc_final: 0.8456 (tmm) REVERT: B 104 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 96 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 171 SER cc_start: 0.8597 (m) cc_final: 0.8307 (p) REVERT: C 525 CYS cc_start: 0.5553 (p) cc_final: 0.5065 (p) REVERT: C 554 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6312 (mm-30) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.2225 time to fit residues: 28.4735 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 207 ASN A 147 GLN C 493 GLN C 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5608 Z= 0.340 Angle : 0.704 8.230 7625 Z= 0.362 Chirality : 0.048 0.151 849 Planarity : 0.005 0.060 990 Dihedral : 6.664 56.311 792 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.29 % Allowed : 8.82 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.32), residues: 709 helix: -2.36 (0.83), residues: 35 sheet: -1.05 (0.32), residues: 266 loop : -1.34 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.003 0.001 HIS A 198 PHE 0.016 0.002 PHE B 103 TYR 0.015 0.002 TYR B 95 ARG 0.004 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.617 Fit side-chains REVERT: B 81 MET cc_start: 0.8893 (tmm) cc_final: 0.8408 (tmm) REVERT: A 177 SER cc_start: 0.8780 (m) cc_final: 0.8401 (t) REVERT: C 554 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6202 (mm-30) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.1559 time to fit residues: 16.8086 Evaluate side-chains 71 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain C residue 345 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 43 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.0670 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5608 Z= 0.234 Angle : 0.629 9.414 7625 Z= 0.320 Chirality : 0.046 0.145 849 Planarity : 0.004 0.049 990 Dihedral : 5.824 57.457 776 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.45 % Allowed : 11.93 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.32), residues: 709 helix: -2.48 (0.79), residues: 35 sheet: -0.72 (0.33), residues: 261 loop : -1.28 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.002 0.001 HIS A 189 PHE 0.015 0.001 PHE B 103 TYR 0.010 0.001 TYR B 95 ARG 0.002 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.565 Fit side-chains REVERT: B 81 MET cc_start: 0.8892 (tmm) cc_final: 0.8455 (tmm) REVERT: B 113 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8362 (pm20) REVERT: A 177 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (t) REVERT: A 181 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7866 (pp) REVERT: C 320 VAL cc_start: 0.2347 (OUTLIER) cc_final: 0.1818 (m) REVERT: C 554 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6277 (mm-30) REVERT: C 592 PHE cc_start: 0.2577 (p90) cc_final: 0.2322 (p90) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.1656 time to fit residues: 17.1647 Evaluate side-chains 75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 5608 Z= 0.403 Angle : 0.721 8.172 7625 Z= 0.366 Chirality : 0.049 0.154 849 Planarity : 0.005 0.046 990 Dihedral : 6.233 57.857 776 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.27 % Allowed : 12.25 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.31), residues: 709 helix: -2.63 (0.75), residues: 35 sheet: -0.61 (0.32), residues: 274 loop : -1.40 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.003 0.001 HIS A 189 PHE 0.021 0.002 PHE B 103 TYR 0.012 0.002 TYR C 369 ARG 0.003 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.626 Fit side-chains REVERT: B 81 MET cc_start: 0.8891 (tmm) cc_final: 0.8442 (tmm) REVERT: B 113 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: A 33 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8617 (tp) REVERT: A 177 SER cc_start: 0.8710 (m) cc_final: 0.8422 (t) REVERT: C 592 PHE cc_start: 0.2816 (p90) cc_final: 0.2361 (p90) outliers start: 20 outliers final: 15 residues processed: 76 average time/residue: 0.1644 time to fit residues: 16.9851 Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 chunk 34 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 39 optimal weight: 0.6980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5608 Z= 0.195 Angle : 0.610 10.697 7625 Z= 0.305 Chirality : 0.045 0.145 849 Planarity : 0.004 0.041 990 Dihedral : 5.684 53.707 776 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.76 % Allowed : 12.09 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.32), residues: 709 helix: -2.51 (0.79), residues: 35 sheet: -0.43 (0.34), residues: 259 loop : -1.20 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.002 0.001 HIS A 189 PHE 0.011 0.001 PHE B 103 TYR 0.010 0.001 TYR B 95 ARG 0.001 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.657 Fit side-chains REVERT: B 81 MET cc_start: 0.8852 (tmm) cc_final: 0.8484 (tmm) REVERT: B 113 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: A 177 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8462 (t) REVERT: C 554 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6622 (pt0) outliers start: 23 outliers final: 15 residues processed: 81 average time/residue: 0.1595 time to fit residues: 17.6360 Evaluate side-chains 77 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5608 Z= 0.413 Angle : 0.733 9.273 7625 Z= 0.366 Chirality : 0.049 0.158 849 Planarity : 0.005 0.041 990 Dihedral : 5.983 55.905 775 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.76 % Allowed : 12.91 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.32), residues: 709 helix: -2.61 (0.78), residues: 35 sheet: -0.43 (0.32), residues: 273 loop : -1.32 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 94 HIS 0.003 0.001 HIS A 189 PHE 0.021 0.002 PHE B 103 TYR 0.014 0.002 TYR B 95 ARG 0.003 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.602 Fit side-chains REVERT: B 10 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: B 81 MET cc_start: 0.8855 (tmm) cc_final: 0.8429 (tmm) REVERT: B 113 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: A 33 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8606 (tp) REVERT: A 177 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8446 (t) REVERT: C 418 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8292 (tt) REVERT: C 519 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.6062 (m-70) outliers start: 23 outliers final: 15 residues processed: 77 average time/residue: 0.1737 time to fit residues: 18.1177 Evaluate side-chains 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 26 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5608 Z= 0.167 Angle : 0.586 7.774 7625 Z= 0.294 Chirality : 0.045 0.145 849 Planarity : 0.004 0.038 990 Dihedral : 5.397 52.951 775 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.59 % Allowed : 13.24 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.32), residues: 709 helix: -2.46 (0.78), residues: 35 sheet: -0.30 (0.33), residues: 263 loop : -1.17 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.001 0.000 HIS A 189 PHE 0.008 0.001 PHE B 103 TYR 0.009 0.001 TYR B 153 ARG 0.002 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.663 Fit side-chains REVERT: B 81 MET cc_start: 0.8815 (tmm) cc_final: 0.8521 (tmm) REVERT: B 113 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: A 82 ASP cc_start: 0.8327 (m-30) cc_final: 0.8102 (m-30) REVERT: A 177 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8479 (t) REVERT: C 554 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6637 (pt0) outliers start: 22 outliers final: 16 residues processed: 81 average time/residue: 0.1609 time to fit residues: 17.6621 Evaluate side-chains 74 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 61 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5608 Z= 0.295 Angle : 0.671 12.883 7625 Z= 0.331 Chirality : 0.047 0.147 849 Planarity : 0.004 0.040 990 Dihedral : 5.345 40.350 775 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.78 % Allowed : 15.20 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.32), residues: 709 helix: -2.51 (0.77), residues: 35 sheet: -0.27 (0.33), residues: 273 loop : -1.20 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.002 0.001 HIS A 189 PHE 0.017 0.002 PHE B 103 TYR 0.012 0.002 TYR B 95 ARG 0.003 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.601 Fit side-chains REVERT: B 81 MET cc_start: 0.8844 (tmm) cc_final: 0.8364 (tmm) REVERT: B 113 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8336 (pt0) REVERT: A 33 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 177 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8451 (t) REVERT: C 390 LEU cc_start: 0.7459 (mt) cc_final: 0.7228 (mt) REVERT: C 554 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6711 (pt0) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.1684 time to fit residues: 16.2488 Evaluate side-chains 74 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 46 optimal weight: 0.5980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5608 Z= 0.201 Angle : 0.606 11.956 7625 Z= 0.300 Chirality : 0.045 0.142 849 Planarity : 0.004 0.038 990 Dihedral : 5.042 41.936 774 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.94 % Allowed : 15.36 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.32), residues: 709 helix: -2.47 (0.77), residues: 35 sheet: -0.20 (0.33), residues: 263 loop : -1.15 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE B 103 TYR 0.009 0.001 TYR A 49 ARG 0.004 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.666 Fit side-chains REVERT: B 10 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: B 81 MET cc_start: 0.8839 (tmm) cc_final: 0.8502 (tmm) REVERT: B 113 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8346 (pt0) REVERT: A 33 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8627 (tp) REVERT: A 82 ASP cc_start: 0.8334 (m-30) cc_final: 0.8123 (m-30) REVERT: A 147 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: A 177 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8469 (t) REVERT: C 554 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6634 (pt0) outliers start: 18 outliers final: 12 residues processed: 70 average time/residue: 0.1799 time to fit residues: 16.7613 Evaluate side-chains 73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 44 optimal weight: 0.0040 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5608 Z= 0.206 Angle : 0.607 11.705 7625 Z= 0.300 Chirality : 0.045 0.142 849 Planarity : 0.004 0.038 990 Dihedral : 4.992 41.499 774 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.94 % Allowed : 15.36 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.32), residues: 709 helix: -2.35 (0.78), residues: 35 sheet: -0.18 (0.33), residues: 263 loop : -1.14 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.003 0.001 HIS A 189 PHE 0.012 0.001 PHE B 103 TYR 0.010 0.001 TYR B 95 ARG 0.009 0.000 ARG A 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1418 Ramachandran restraints generated. 709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.626 Fit side-chains REVERT: B 10 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: B 81 MET cc_start: 0.8862 (tmm) cc_final: 0.8502 (tmm) REVERT: B 113 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: A 33 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 82 ASP cc_start: 0.8334 (m-30) cc_final: 0.8122 (m-30) REVERT: A 147 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6512 (mt0) REVERT: A 177 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8483 (t) REVERT: C 554 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6626 (pt0) outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.1662 time to fit residues: 15.8795 Evaluate side-chains 75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** 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 = 0.3732 r_free = 0.3732 target = 0.149169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119806 restraints weight = 7056.115| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.20 r_work: 0.3283 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5608 Z= 0.373 Angle : 0.716 13.860 7625 Z= 0.354 Chirality : 0.048 0.154 849 Planarity : 0.005 0.039 990 Dihedral : 5.513 40.320 774 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.94 % Allowed : 15.69 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.32), residues: 709 helix: -2.34 (0.80), residues: 35 sheet: -0.23 (0.33), residues: 272 loop : -1.22 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 47 HIS 0.003 0.001 HIS A 189 PHE 0.019 0.002 PHE B 103 TYR 0.014 0.002 TYR B 95 ARG 0.003 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.00 seconds wall clock time: 33 minutes 2.28 seconds (1982.28 seconds total)