Starting phenix.real_space_refine on Thu Jun 5 06:33:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wh8_32497/06_2025/7wh8_32497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wh8_32497/06_2025/7wh8_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_32497/06_2025/7wh8_32497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wh8_32497/06_2025/7wh8_32497.map" model { file = "/net/cci-nas-00/data/ceres_data/7wh8_32497/06_2025/7wh8_32497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wh8_32497/06_2025/7wh8_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.18, per 1000 atoms: 0.76 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: 1.23 Conformation dependent library (CDL) restraints added in 667.8 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: 0.72 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: 1.71 Time building geometry restraints manager: 1.49 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.370 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- 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 5617 Z= 0.189 Angle : 0.711 11.555 7643 Z= 0.399 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 Details of bonding type rmsd hydrogen bonds : bond 0.29344 ( 161) hydrogen bonds : angle 11.82974 ( 441) SS BOND : bond 0.00638 ( 9) SS BOND : angle 1.34996 ( 18) covalent geometry : bond 0.00364 ( 5608) covalent geometry : angle 0.70896 ( 7625) *********************** 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 : 0.645 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: 0.1998 time to fit residues: 25.6162 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 : 0.631 ------------------------------------------------------------------------------- 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: 0.0980 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: 0.0980 chunk 63 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127549 restraints weight = 7057.852| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.13 r_work: 0.3393 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5617 Z= 0.157 Angle : 0.651 7.449 7643 Z= 0.336 Chirality : 0.047 0.153 849 Planarity : 0.005 0.059 990 Dihedral : 6.393 58.625 792 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.63 % Allowed : 8.99 % Favored : 89.38 % 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: -1.81 (0.32), residues: 709 helix: -2.32 (0.84), residues: 35 sheet: -0.93 (0.34), residues: 248 loop : -1.26 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS A 189 PHE 0.014 0.002 PHE B 103 TYR 0.012 0.002 TYR C 421 ARG 0.003 0.000 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 161) hydrogen bonds : angle 7.24815 ( 441) SS BOND : bond 0.00626 ( 9) SS BOND : angle 1.19266 ( 18) covalent geometry : bond 0.00374 ( 5608) covalent geometry : angle 0.64901 ( 7625) *********************** 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 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.512 Fit side-chains REVERT: B 81 MET cc_start: 0.9096 (tmm) cc_final: 0.8705 (tmm) REVERT: B 113 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: A 177 SER cc_start: 0.8946 (m) cc_final: 0.8622 (t) REVERT: C 554 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6183 (mm-30) outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.1550 time to fit residues: 16.5221 Evaluate side-chains 70 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 147 GLN Chi-restraints excluded: chain C residue 320 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 0.0670 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122031 restraints weight = 7103.592| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.15 r_work: 0.3328 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5617 Z= 0.240 Angle : 0.720 9.789 7643 Z= 0.365 Chirality : 0.048 0.154 849 Planarity : 0.005 0.051 990 Dihedral : 6.089 55.500 776 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.27 % Allowed : 11.60 % Favored : 85.13 % 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: -1.81 (0.31), residues: 709 helix: -2.52 (0.78), residues: 35 sheet: -0.69 (0.33), residues: 261 loop : -1.42 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.002 0.001 HIS A 198 PHE 0.023 0.002 PHE B 103 TYR 0.013 0.002 TYR B 95 ARG 0.006 0.001 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 161) hydrogen bonds : angle 6.77354 ( 441) SS BOND : bond 0.00677 ( 9) SS BOND : angle 1.48139 ( 18) covalent geometry : bond 0.00583 ( 5608) covalent geometry : angle 0.71678 ( 7625) *********************** 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 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.663 Fit side-chains REVERT: B 81 MET cc_start: 0.9169 (tmm) cc_final: 0.8583 (tmm) REVERT: A 177 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8583 (t) REVERT: A 181 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7964 (pp) REVERT: C 554 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6297 (mm-30) REVERT: C 592 PHE cc_start: 0.3705 (p90) cc_final: 0.2934 (p90) outliers start: 20 outliers final: 12 residues processed: 77 average time/residue: 0.1639 time to fit residues: 17.1871 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 : 0.640 ------------------------------------------------------------------------------- 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 159 THR 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 345 THR 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 21 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.0060 chunk 68 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.2312 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130145 restraints weight = 7192.682| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.19 r_work: 0.3408 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5617 Z= 0.113 Angle : 0.581 10.116 7643 Z= 0.294 Chirality : 0.044 0.142 849 Planarity : 0.004 0.043 990 Dihedral : 5.300 51.817 776 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.96 % Allowed : 13.24 % Favored : 84.80 % 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: -1.51 (0.32), residues: 709 helix: -2.44 (0.81), residues: 35 sheet: -0.50 (0.33), residues: 259 loop : -1.19 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.001 0.001 HIS A 189 PHE 0.008 0.001 PHE B 103 TYR 0.010 0.001 TYR C 453 ARG 0.003 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 161) hydrogen bonds : angle 6.14100 ( 441) SS BOND : bond 0.00436 ( 9) SS BOND : angle 0.79563 ( 18) covalent geometry : bond 0.00263 ( 5608) covalent geometry : angle 0.58082 ( 7625) *********************** 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 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.703 Fit side-chains REVERT: B 31 ASN cc_start: 0.8019 (m-40) cc_final: 0.7792 (m110) REVERT: B 81 MET cc_start: 0.9117 (tmm) cc_final: 0.8777 (tmm) REVERT: B 113 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: A 177 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8625 (t) REVERT: A 181 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7905 (pp) REVERT: C 320 VAL cc_start: 0.3537 (OUTLIER) cc_final: 0.3085 (t) REVERT: C 554 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6234 (mm-30) REVERT: C 592 PHE cc_start: 0.3318 (p90) cc_final: 0.2701 (p90) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.1633 time to fit residues: 18.5535 Evaluate side-chains 75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 A residue 63 ILE 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 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 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 66 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125376 restraints weight = 7072.472| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.15 r_work: 0.3376 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5617 Z= 0.156 Angle : 0.627 11.370 7643 Z= 0.313 Chirality : 0.046 0.142 849 Planarity : 0.004 0.041 990 Dihedral : 5.023 38.154 774 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.43 % Allowed : 13.07 % Favored : 83.50 % 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: -1.40 (0.32), residues: 709 helix: -2.50 (0.79), residues: 35 sheet: -0.40 (0.33), residues: 269 loop : -1.13 (0.31), residues: 405 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 0.001 PHE B 103 TYR 0.011 0.001 TYR B 95 ARG 0.002 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 161) hydrogen bonds : angle 6.03010 ( 441) SS BOND : bond 0.00551 ( 9) SS BOND : angle 1.15522 ( 18) covalent geometry : bond 0.00377 ( 5608) covalent geometry : angle 0.62485 ( 7625) *********************** 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 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.679 Fit side-chains REVERT: B 81 MET cc_start: 0.9175 (tmm) cc_final: 0.8716 (tmm) REVERT: B 113 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8584 (pt0) REVERT: A 13 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 33 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8773 (tp) REVERT: A 82 ASP cc_start: 0.8739 (m-30) cc_final: 0.8465 (m-30) REVERT: A 177 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8607 (t) REVERT: C 320 VAL cc_start: 0.3922 (OUTLIER) cc_final: 0.3545 (t) REVERT: C 554 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6655 (pt0) REVERT: C 592 PHE cc_start: 0.3452 (p90) cc_final: 0.2775 (p90) outliers start: 21 outliers final: 10 residues processed: 79 average time/residue: 0.1518 time to fit residues: 16.5690 Evaluate side-chains 77 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 13 LEU 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 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 27 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 34 optimal weight: 0.0020 chunk 56 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126808 restraints weight = 7007.969| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.18 r_work: 0.3364 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5617 Z= 0.131 Angle : 0.587 9.411 7643 Z= 0.294 Chirality : 0.045 0.141 849 Planarity : 0.004 0.039 990 Dihedral : 4.879 38.891 774 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.43 % Allowed : 13.07 % Favored : 83.50 % 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: -2.56 (0.77), residues: 35 sheet: -0.31 (0.33), residues: 259 loop : -1.06 (0.31), residues: 415 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 0.013 0.001 PHE B 103 TYR 0.010 0.001 TYR B 95 ARG 0.002 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 161) hydrogen bonds : angle 5.86973 ( 441) SS BOND : bond 0.00524 ( 9) SS BOND : angle 1.03995 ( 18) covalent geometry : bond 0.00315 ( 5608) covalent geometry : angle 0.58565 ( 7625) *********************** 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 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.599 Fit side-chains REVERT: B 81 MET cc_start: 0.9143 (tmm) cc_final: 0.8759 (tmm) REVERT: B 113 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: A 13 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.8520 (m-30) REVERT: A 177 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8610 (t) REVERT: C 554 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6630 (pt0) REVERT: C 592 PHE cc_start: 0.3296 (p90) cc_final: 0.2733 (p90) outliers start: 21 outliers final: 13 residues processed: 79 average time/residue: 0.1487 time to fit residues: 16.2103 Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 13 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120985 restraints weight = 7178.211| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.17 r_work: 0.3287 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5617 Z= 0.262 Angle : 0.753 12.704 7643 Z= 0.372 Chirality : 0.049 0.158 849 Planarity : 0.005 0.040 990 Dihedral : 5.665 39.153 774 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.43 % Allowed : 14.05 % Favored : 82.52 % 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: -1.47 (0.32), residues: 709 helix: -2.64 (0.78), residues: 35 sheet: -0.35 (0.32), residues: 273 loop : -1.26 (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 0.004 0.001 ARG B 50 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 161) hydrogen bonds : angle 6.22993 ( 441) SS BOND : bond 0.00837 ( 9) SS BOND : angle 2.00007 ( 18) covalent geometry : bond 0.00638 ( 5608) covalent geometry : angle 0.74718 ( 7625) *********************** 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 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.605 Fit side-chains REVERT: B 10 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: B 81 MET cc_start: 0.9148 (tmm) cc_final: 0.8697 (tmm) REVERT: B 113 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: A 33 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 177 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8580 (t) REVERT: C 390 LEU cc_start: 0.7475 (mt) cc_final: 0.7270 (mt) outliers start: 21 outliers final: 13 residues processed: 74 average time/residue: 0.1594 time to fit residues: 16.0193 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 : 0.710 ------------------------------------------------------------------------------- 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 127 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 345 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 26 optimal weight: 0.0030 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123555 restraints weight = 7048.177| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.16 r_work: 0.3318 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5617 Z= 0.182 Angle : 0.671 11.857 7643 Z= 0.332 Chirality : 0.047 0.143 849 Planarity : 0.004 0.038 990 Dihedral : 5.383 41.765 774 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.45 % Allowed : 15.03 % Favored : 82.52 % 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: -1.46 (0.32), residues: 709 helix: -2.53 (0.80), residues: 35 sheet: -0.30 (0.33), residues: 262 loop : -1.29 (0.31), residues: 412 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 0.016 0.002 PHE B 103 TYR 0.012 0.002 TYR B 95 ARG 0.003 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 161) hydrogen bonds : angle 6.08385 ( 441) SS BOND : bond 0.00637 ( 9) SS BOND : angle 1.50405 ( 18) covalent geometry : bond 0.00439 ( 5608) covalent geometry : angle 0.66751 ( 7625) *********************** 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: 15 poor density : 60 time to evaluate : 0.679 Fit side-chains REVERT: B 81 MET cc_start: 0.9149 (tmm) cc_final: 0.8707 (tmm) REVERT: B 113 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: A 33 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8809 (tp) REVERT: A 177 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8621 (t) REVERT: C 554 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6734 (pt0) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.1583 time to fit residues: 15.6782 Evaluate side-chains 73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125595 restraints weight = 7038.597| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.19 r_work: 0.3361 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5617 Z= 0.120 Angle : 0.595 10.770 7643 Z= 0.296 Chirality : 0.045 0.142 849 Planarity : 0.004 0.038 990 Dihedral : 4.955 43.602 774 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.78 % Allowed : 15.36 % Favored : 81.86 % 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: -1.32 (0.32), residues: 709 helix: -2.39 (0.83), residues: 34 sheet: -0.22 (0.33), residues: 263 loop : -1.17 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.002 0.001 HIS A 189 PHE 0.009 0.001 PHE B 103 TYR 0.010 0.001 TYR C 453 ARG 0.004 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 161) hydrogen bonds : angle 5.78441 ( 441) SS BOND : bond 0.00522 ( 9) SS BOND : angle 1.20820 ( 18) covalent geometry : bond 0.00284 ( 5608) covalent geometry : angle 0.59324 ( 7625) *********************** 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 78 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.653 Fit side-chains REVERT: B 81 MET cc_start: 0.9052 (tmm) cc_final: 0.8734 (tmm) REVERT: B 113 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8622 (pt0) REVERT: A 33 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8845 (tp) REVERT: A 82 ASP cc_start: 0.8763 (m-30) cc_final: 0.8496 (m-30) REVERT: A 177 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8612 (t) REVERT: C 554 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6559 (pt0) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.1636 time to fit residues: 17.0426 Evaluate side-chains 72 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 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 63 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 43 GLN ** A 147 GLN ** 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 = 0.3729 r_free = 0.3729 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120192 restraints weight = 7049.017| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.20 r_work: 0.3293 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5617 Z= 0.237 Angle : 0.732 14.650 7643 Z= 0.360 Chirality : 0.049 0.154 849 Planarity : 0.004 0.039 990 Dihedral : 5.563 42.447 774 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.61 % Allowed : 15.52 % Favored : 81.86 % 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: -1.45 (0.32), residues: 709 helix: -2.49 (0.78), residues: 35 sheet: -0.27 (0.33), residues: 262 loop : -1.29 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 94 HIS 0.002 0.001 HIS A 189 PHE 0.020 0.002 PHE B 103 TYR 0.015 0.002 TYR B 95 ARG 0.009 0.001 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 161) hydrogen bonds : angle 6.11013 ( 441) SS BOND : bond 0.00673 ( 9) SS BOND : angle 1.67922 ( 18) covalent geometry : bond 0.00576 ( 5608) covalent geometry : angle 0.72842 ( 7625) ********************** 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 72 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.603 Fit side-chains REVERT: B 81 MET cc_start: 0.9157 (tmm) cc_final: 0.8744 (tmm) REVERT: B 113 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8697 (pt0) REVERT: A 33 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8778 (tp) REVERT: A 143 GLU cc_start: 0.8334 (tp30) cc_final: 0.8108 (mp0) REVERT: A 177 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8521 (t) REVERT: C 418 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8394 (tt) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 0.1622 time to fit residues: 15.3943 Evaluate side-chains 72 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 418 ILE 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 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121648 restraints weight = 7187.584| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.19 r_work: 0.3300 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5617 Z= 0.217 Angle : 0.703 13.809 7643 Z= 0.348 Chirality : 0.048 0.145 849 Planarity : 0.004 0.039 990 Dihedral : 5.544 43.388 774 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.78 % Allowed : 15.52 % 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: -1.47 (0.32), residues: 709 helix: -2.47 (0.78), residues: 35 sheet: -0.27 (0.33), residues: 263 loop : -1.32 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 94 HIS 0.003 0.001 HIS A 189 PHE 0.017 0.002 PHE B 103 TYR 0.013 0.002 TYR B 95 ARG 0.009 0.001 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 161) hydrogen bonds : angle 6.11303 ( 441) SS BOND : bond 0.00659 ( 9) SS BOND : angle 1.54652 ( 18) covalent geometry : bond 0.00527 ( 5608) covalent geometry : angle 0.70005 ( 7625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.47 seconds wall clock time: 65 minutes 52.19 seconds (3952.19 seconds total)