Starting phenix.real_space_refine on Tue Feb 13 10:46:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wh8_32497/02_2024/7wh8_32497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wh8_32497/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wh8_32497/02_2024/7wh8_32497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wh8_32497/02_2024/7wh8_32497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wh8_32497/02_2024/7wh8_32497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wh8_32497/02_2024/7wh8_32497.pdb" } 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 Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.52, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.69 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: 1.55 Time building geometry restraints manager: 2.53 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: 100.15 - 106.92: 181 106.92 - 113.69: 3031 113.69 - 120.46: 1961 120.46 - 127.23: 2399 127.23 - 134.00: 53 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 2.440 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 2.440 nonbonded pdb=" O LEU A 13 " pdb=" N LYS A 107 " model vdw 2.288 2.520 nonbonded pdb=" O SER B 223 " pdb=" OG SER B 223 " model vdw 2.299 2.440 ... (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 ========== 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: 1.890 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: 9.200 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.530 Find NCS groups from input model: 0.150 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.650 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.703 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: 0.1880 time to fit residues: 23.8486 Evaluate side-chains 81 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 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 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: 0.9980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5608 Z= 0.354 Angle : 0.702 8.700 7625 Z= 0.360 Chirality : 0.048 0.151 849 Planarity : 0.005 0.060 990 Dihedral : 6.628 56.706 792 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.29 % Allowed : 9.48 % Favored : 88.24 % 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: -1.94 (0.32), residues: 709 helix: -2.25 (0.86), residues: 35 sheet: -1.06 (0.32), residues: 263 loop : -1.33 (0.31), residues: 411 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 0.017 0.002 PHE B 103 TYR 0.013 0.002 TYR B 95 ARG 0.005 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 78 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.655 Fit side-chains REVERT: B 81 MET cc_start: 0.8899 (tmm) cc_final: 0.8344 (tmm) REVERT: A 27 GLN cc_start: 0.8103 (tt0) cc_final: 0.7839 (tt0) REVERT: A 177 SER cc_start: 0.8795 (m) cc_final: 0.8412 (t) REVERT: C 554 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6206 (mm-30) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.1565 time to fit residues: 16.0122 Evaluate side-chains 70 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 28 SER 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 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: 0.9990 chunk 19 optimal weight: 0.0870 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.0270 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.0270 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1643 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= 0.186 Angle : 0.593 8.826 7625 Z= 0.299 Chirality : 0.044 0.145 849 Planarity : 0.004 0.048 990 Dihedral : 5.657 59.884 775 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.96 % Allowed : 12.75 % Favored : 85.29 % 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: -1.69 (0.32), residues: 709 helix: -2.09 (0.88), residues: 35 sheet: -0.70 (0.34), residues: 240 loop : -1.28 (0.30), residues: 434 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 0.010 0.001 PHE B 103 TYR 0.009 0.001 TYR C 453 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 77 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.596 Fit side-chains REVERT: B 81 MET cc_start: 0.8908 (tmm) cc_final: 0.8424 (tmm) REVERT: B 113 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: A 177 SER cc_start: 0.8649 (m) cc_final: 0.8437 (t) REVERT: A 181 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7945 (pp) REVERT: C 554 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6254 (mm-30) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.1636 time to fit residues: 16.3322 Evaluate side-chains 71 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 181 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5608 Z= 0.358 Angle : 0.684 8.031 7625 Z= 0.345 Chirality : 0.047 0.153 849 Planarity : 0.005 0.045 990 Dihedral : 5.921 56.664 775 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.10 % Allowed : 13.56 % 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: -1.67 (0.31), residues: 709 helix: -2.04 (0.86), residues: 35 sheet: -0.58 (0.32), residues: 263 loop : -1.37 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 94 HIS 0.002 0.001 HIS A 189 PHE 0.018 0.002 PHE B 103 TYR 0.014 0.002 TYR B 95 ARG 0.003 0.000 ARG C 567 *********************** 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 80 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.609 Fit side-chains REVERT: B 81 MET cc_start: 0.8923 (tmm) cc_final: 0.8322 (tmm) REVERT: A 177 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8346 (t) REVERT: C 592 PHE cc_start: 0.2779 (p90) cc_final: 0.2417 (p90) outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.1557 time to fit residues: 16.0090 Evaluate side-chains 76 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 398 ASP 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: 0.3980 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5608 Z= 0.281 Angle : 0.638 7.108 7625 Z= 0.321 Chirality : 0.046 0.145 849 Planarity : 0.004 0.044 990 Dihedral : 5.713 51.519 775 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.59 % Allowed : 12.42 % Favored : 83.99 % 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: -1.60 (0.32), residues: 709 helix: -2.12 (0.84), residues: 35 sheet: -0.50 (0.33), residues: 257 loop : -1.34 (0.31), residues: 417 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 0.015 0.001 PHE B 103 TYR 0.012 0.002 TYR B 95 ARG 0.002 0.000 ARG B 38 *********************** 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 81 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.646 Fit side-chains REVERT: B 81 MET cc_start: 0.8884 (tmm) cc_final: 0.8411 (tmm) REVERT: B 113 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: A 33 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 177 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8333 (t) REVERT: C 554 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6711 (pt0) REVERT: C 592 PHE cc_start: 0.2612 (p90) cc_final: 0.2265 (p90) outliers start: 22 outliers final: 15 residues processed: 76 average time/residue: 0.1590 time to fit residues: 16.5332 Evaluate side-chains 75 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 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 177 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 494 SER 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: 0.0020 chunk 67 optimal weight: 0.0030 chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 overall best weight: 0.2398 ------------------------------------------------------------------------------- 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 C 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5608 Z= 0.167 Angle : 0.576 10.399 7625 Z= 0.283 Chirality : 0.044 0.143 849 Planarity : 0.004 0.039 990 Dihedral : 5.068 44.429 775 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.94 % Allowed : 13.56 % 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: -2.02 (0.86), residues: 35 sheet: -0.33 (0.35), residues: 245 loop : -1.21 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.002 0.000 HIS A 189 PHE 0.009 0.001 PHE B 103 TYR 0.009 0.001 TYR C 453 ARG 0.003 0.000 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 fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.134 Fit side-chains REVERT: B 81 MET cc_start: 0.8846 (tmm) cc_final: 0.8517 (tmm) REVERT: B 113 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: A 33 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8659 (tp) REVERT: A 177 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8379 (t) REVERT: C 554 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6606 (pt0) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 0.1852 time to fit residues: 19.7884 Evaluate side-chains 72 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 398 ASP 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 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2345 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= 0.297 Angle : 0.657 9.525 7625 Z= 0.328 Chirality : 0.046 0.148 849 Planarity : 0.004 0.039 990 Dihedral : 5.330 46.373 774 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.43 % Allowed : 13.56 % Favored : 83.01 % 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: -1.39 (0.32), residues: 709 helix: -2.06 (0.85), residues: 35 sheet: -0.26 (0.33), residues: 257 loop : -1.26 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.002 0.001 HIS A 189 PHE 0.017 0.002 PHE B 103 TYR 0.013 0.002 TYR B 95 ARG 0.003 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 79 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.633 Fit side-chains REVERT: B 10 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: B 81 MET cc_start: 0.8888 (tmm) cc_final: 0.8392 (tmm) REVERT: B 113 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: A 33 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8582 (tp) REVERT: A 177 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8361 (t) REVERT: C 592 PHE cc_start: 0.2454 (p90) cc_final: 0.2163 (p90) outliers start: 21 outliers final: 15 residues processed: 74 average time/residue: 0.1648 time to fit residues: 16.5906 Evaluate side-chains 74 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 494 SER 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: 0.0870 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 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 C 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5608 Z= 0.198 Angle : 0.603 8.495 7625 Z= 0.300 Chirality : 0.045 0.143 849 Planarity : 0.004 0.038 990 Dihedral : 5.110 47.557 774 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.59 % Allowed : 14.05 % Favored : 82.35 % 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: -1.29 (0.32), residues: 709 helix: -2.03 (0.85), residues: 35 sheet: -0.19 (0.34), residues: 249 loop : -1.17 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.002 0.000 HIS A 189 PHE 0.012 0.001 PHE B 103 TYR 0.011 0.001 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 80 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.692 Fit side-chains REVERT: B 81 MET cc_start: 0.8866 (tmm) cc_final: 0.8501 (tmm) REVERT: B 113 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: A 33 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8613 (tp) REVERT: A 177 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8414 (t) REVERT: C 418 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8209 (tt) REVERT: C 554 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6710 (pt0) outliers start: 22 outliers final: 13 residues processed: 75 average time/residue: 0.1591 time to fit residues: 16.3490 Evaluate side-chains 73 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 147 GLN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 418 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5608 Z= 0.337 Angle : 0.681 8.436 7625 Z= 0.340 Chirality : 0.047 0.152 849 Planarity : 0.004 0.039 990 Dihedral : 5.504 47.255 774 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.43 % Allowed : 14.54 % 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: -1.42 (0.32), residues: 709 helix: -2.08 (0.84), residues: 35 sheet: -0.26 (0.34), residues: 251 loop : -1.28 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 47 HIS 0.003 0.001 HIS A 189 PHE 0.017 0.002 PHE B 103 TYR 0.014 0.002 TYR B 95 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 76 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.636 Fit side-chains REVERT: B 10 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: B 81 MET cc_start: 0.8874 (tmm) cc_final: 0.8362 (tmm) REVERT: A 33 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8613 (tp) REVERT: A 177 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8458 (t) REVERT: C 418 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8465 (mm) outliers start: 21 outliers final: 13 residues processed: 72 average time/residue: 0.1662 time to fit residues: 16.1976 Evaluate side-chains 71 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 177 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 494 SER 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: 0.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 0.0370 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5608 Z= 0.304 Angle : 0.660 8.220 7625 Z= 0.330 Chirality : 0.047 0.142 849 Planarity : 0.004 0.038 990 Dihedral : 5.454 46.928 774 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % 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: -1.42 (0.32), residues: 709 helix: -2.08 (0.84), residues: 35 sheet: -0.16 (0.34), residues: 246 loop : -1.35 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS A 189 PHE 0.016 0.002 PHE B 103 TYR 0.013 0.002 TYR B 95 ARG 0.004 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 71 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.652 Fit side-chains REVERT: B 10 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: B 81 MET cc_start: 0.8869 (tmm) cc_final: 0.8404 (tmm) REVERT: A 33 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8618 (tp) REVERT: A 177 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8324 (t) outliers start: 17 outliers final: 12 residues processed: 67 average time/residue: 0.1548 time to fit residues: 14.1780 Evaluate side-chains 72 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 177 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 494 SER 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: 0.7980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 10 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN C 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123851 restraints weight = 7046.246| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.15 r_work: 0.3337 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5608 Z= 0.215 Angle : 0.603 7.784 7625 Z= 0.302 Chirality : 0.045 0.141 849 Planarity : 0.004 0.038 990 Dihedral : 5.143 48.133 774 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % 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: -1.32 (0.32), residues: 709 helix: -2.01 (0.85), residues: 35 sheet: -0.09 (0.34), residues: 249 loop : -1.28 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.004 0.001 HIS A 189 PHE 0.012 0.001 PHE B 103 TYR 0.010 0.001 TYR B 95 ARG 0.004 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.42 seconds wall clock time: 30 minutes 53.33 seconds (1853.33 seconds total)