Starting phenix.real_space_refine on Tue Feb 13 20:16:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f40_31443/02_2024/7f40_31443_updated.pdb" } resolution = 3.49 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= 0.006 sd= 0.068 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 48 5.16 5 C 5098 2.51 5 N 1162 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 7596 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3675 Classifications: {'peptide': 449} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 430} Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3675 Classifications: {'peptide': 449} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 430} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3IX': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3IX': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.65, per 1000 atoms: 0.61 Number of scatterers: 7596 At special positions: 0 Unit cell: (112.66, 117.82, 75.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 8 15.00 O 1280 8.00 N 1162 7.00 C 5098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.93 Conformation dependent library (CDL) restraints added in 1.3 seconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 0 sheets defined 60.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 53 through 74 removed outlier: 3.645A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 104 through 119 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.623A pdb=" N PHE A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 177 removed outlier: 3.670A pdb=" N GLY A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.983A pdb=" N TYR A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 345 through 348 No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 373 through 388 removed outlier: 4.028A pdb=" N HIS A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 414 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 442 through 454 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 458 through 468 removed outlier: 4.236A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 489 Proline residue: A 484 - end of helix Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 53 through 74 removed outlier: 3.645A pdb=" N ARG B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.623A pdb=" N PHE B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 177 removed outlier: 3.670A pdb=" N GLY B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 243 through 262 Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 294 through 312 removed outlier: 3.983A pdb=" N TYR B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 345 through 348 No H-bonds generated for 'chain 'B' and resid 345 through 348' Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 373 through 388 removed outlier: 4.028A pdb=" N HIS B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 414 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 442 through 454 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 458 through 468 removed outlier: 4.236A pdb=" N SER B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 489 Proline residue: B 484 - end of helix 340 hydrogen bonds defined for protein. 1020 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: 1.94 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1080 1.30 - 1.43: 2375 1.43 - 1.57: 4273 1.57 - 1.70: 16 1.70 - 1.83: 80 Bond restraints: 7824 Sorted by residual: bond pdb=" C48 3IX B 601 " pdb=" C49 3IX B 601 " ideal model delta sigma weight residual 1.541 1.292 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C48 3IX A 601 " pdb=" C49 3IX A 601 " ideal model delta sigma weight residual 1.541 1.293 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C49 3IX A 601 " pdb=" C50 3IX A 601 " ideal model delta sigma weight residual 1.329 1.522 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C49 3IX B 601 " pdb=" C50 3IX B 601 " ideal model delta sigma weight residual 1.329 1.522 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C47 3IX A 601 " pdb=" C48 3IX A 601 " ideal model delta sigma weight residual 1.408 1.512 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 7819 not shown) Histogram of bond angle deviations from ideal: 100.05 - 110.57: 2207 110.57 - 121.09: 6617 121.09 - 131.61: 1768 131.61 - 142.13: 28 142.13 - 152.64: 2 Bond angle restraints: 10622 Sorted by residual: angle pdb=" C51 3IX A 601 " pdb=" N53 3IX A 601 " pdb=" C61 3IX A 601 " ideal model delta sigma weight residual 47.13 125.99 -78.86 3.00e+00 1.11e-01 6.91e+02 angle pdb=" C51 3IX B 601 " pdb=" N53 3IX B 601 " pdb=" C61 3IX B 601 " ideal model delta sigma weight residual 47.13 125.97 -78.84 3.00e+00 1.11e-01 6.91e+02 angle pdb=" C06 3IX A 601 " pdb=" C07 3IX A 601 " pdb=" C08 3IX A 601 " ideal model delta sigma weight residual 152.67 108.48 44.19 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C06 3IX B 601 " pdb=" C07 3IX B 601 " pdb=" C08 3IX B 601 " ideal model delta sigma weight residual 152.67 108.48 44.19 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C09 3IX B 601 " pdb=" C10 3IX B 601 " pdb=" C11 3IX B 601 " ideal model delta sigma weight residual 152.66 113.29 39.37 3.00e+00 1.11e-01 1.72e+02 ... (remaining 10617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 4322 35.80 - 71.61: 140 71.61 - 107.41: 18 107.41 - 143.22: 2 143.22 - 179.02: 4 Dihedral angle restraints: 4486 sinusoidal: 1850 harmonic: 2636 Sorted by residual: dihedral pdb=" N25 3IX B 601 " pdb=" C23 3IX B 601 " pdb=" C24 3IX B 601 " pdb=" S22 3IX B 601 " ideal model delta sinusoidal sigma weight residual 186.30 7.28 179.02 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N25 3IX A 601 " pdb=" C23 3IX A 601 " pdb=" C24 3IX A 601 " pdb=" S22 3IX A 601 " ideal model delta sinusoidal sigma weight residual 186.30 7.28 179.02 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PCW B 602 " pdb=" C4 PCW B 602 " pdb=" C5 PCW B 602 " pdb=" O4P PCW B 602 " ideal model delta sinusoidal sigma weight residual -66.66 79.48 -146.14 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 4483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 841 0.042 - 0.083: 253 0.083 - 0.125: 58 0.125 - 0.166: 6 0.166 - 0.208: 6 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C2 PCW A 602 " pdb=" C1 PCW A 602 " pdb=" C3 PCW A 602 " pdb=" O2 PCW A 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C2 PCW B 602 " pdb=" C1 PCW B 602 " pdb=" C3 PCW B 602 " pdb=" O2 PCW B 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C48 3IX B 601 " pdb=" C47 3IX B 601 " pdb=" C49 3IX B 601 " pdb=" O52 3IX B 601 " both_signs ideal model delta sigma weight residual False 2.69 2.52 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 1161 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 179 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 180 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 179 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 180 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 234 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.025 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2206 2.81 - 3.34: 7476 3.34 - 3.86: 11801 3.86 - 4.38: 12477 4.38 - 4.90: 21792 Nonbonded interactions: 55752 Sorted by model distance: nonbonded pdb=" OG SER A 107 " pdb=" OH TYR A 206 " model vdw 2.293 2.440 nonbonded pdb=" OG SER B 107 " pdb=" OH TYR B 206 " model vdw 2.293 2.440 nonbonded pdb=" N25 3IX A 601 " pdb=" S22 3IX A 601 " model vdw 2.307 2.784 nonbonded pdb=" N25 3IX B 601 " pdb=" S22 3IX B 601 " model vdw 2.307 2.784 nonbonded pdb=" NH1 ARG A 283 " pdb=" OG SER A 467 " model vdw 2.310 2.520 ... (remaining 55747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.580 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.700 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.008 0.249 7824 Z= 0.480 Angle : 1.914 78.859 10622 Z= 0.689 Chirality : 0.043 0.208 1164 Planarity : 0.005 0.067 1272 Dihedral : 18.494 179.021 2806 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.42 (0.29), residues: 894 helix: 1.11 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.73 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 290 HIS 0.002 0.001 HIS B 159 PHE 0.018 0.001 PHE B 115 TYR 0.017 0.001 TYR B 143 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6540 (ptt90) REVERT: B 416 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6746 (mtt90) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1605 time to fit residues: 34.1506 Evaluate side-chains 132 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7824 Z= 0.163 Angle : 0.830 31.720 10622 Z= 0.350 Chirality : 0.039 0.166 1164 Planarity : 0.004 0.048 1272 Dihedral : 16.535 161.531 1142 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 1.39 % Allowed : 10.23 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.13 (0.29), residues: 894 helix: 1.40 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.69 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 461 HIS 0.003 0.001 HIS B 473 PHE 0.011 0.001 PHE B 351 TYR 0.018 0.001 TYR B 269 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.892 Fit side-chains REVERT: A 400 MET cc_start: 0.7028 (tpp) cc_final: 0.6464 (tpp) REVERT: A 416 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6600 (ptt90) REVERT: B 136 MET cc_start: 0.8339 (mmm) cc_final: 0.8099 (mmp) REVERT: B 400 MET cc_start: 0.7012 (tpp) cc_final: 0.6648 (tpt) REVERT: B 416 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6539 (ptt90) outliers start: 11 outliers final: 3 residues processed: 148 average time/residue: 0.1659 time to fit residues: 34.7229 Evaluate side-chains 139 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 64 optimal weight: 4.9990 overall best weight: 1.2280 ------------------------------------------------------------------------------- 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: 0.7698 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7824 Z= 0.229 Angle : 0.828 32.846 10622 Z= 0.355 Chirality : 0.041 0.165 1164 Planarity : 0.004 0.044 1272 Dihedral : 16.196 160.599 1142 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.65 % Allowed : 15.66 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.18 (0.29), residues: 894 helix: 1.37 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.77 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 461 HIS 0.005 0.002 HIS B 159 PHE 0.011 0.001 PHE B 364 TYR 0.013 0.001 TYR A 465 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.772 Fit side-chains REVERT: A 219 MET cc_start: 0.8357 (tpp) cc_final: 0.7794 (tpp) REVERT: A 416 ARG cc_start: 0.7021 (mtt180) cc_final: 0.6343 (ttp-170) REVERT: B 219 MET cc_start: 0.8308 (tpp) cc_final: 0.7756 (tpp) REVERT: B 416 ARG cc_start: 0.7129 (mtt90) cc_final: 0.6587 (ptt90) outliers start: 21 outliers final: 17 residues processed: 154 average time/residue: 0.1666 time to fit residues: 36.4115 Evaluate side-chains 158 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7824 Z= 0.193 Angle : 0.808 32.105 10622 Z= 0.342 Chirality : 0.039 0.180 1164 Planarity : 0.004 0.044 1272 Dihedral : 15.824 157.090 1142 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.04 % Allowed : 18.31 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.04 (0.29), residues: 894 helix: 1.48 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.79 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.003 0.001 HIS A 159 PHE 0.009 0.001 PHE B 105 TYR 0.014 0.001 TYR B 465 ARG 0.004 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 0.840 Fit side-chains REVERT: A 136 MET cc_start: 0.8180 (mmm) cc_final: 0.7864 (mmt) REVERT: A 250 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 367 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7859 (tt) REVERT: A 414 LEU cc_start: 0.8269 (tt) cc_final: 0.7733 (tp) REVERT: A 416 ARG cc_start: 0.7008 (mtt180) cc_final: 0.6632 (ptt90) REVERT: A 417 ASP cc_start: 0.8445 (t0) cc_final: 0.8226 (t0) REVERT: B 367 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7867 (tt) REVERT: B 416 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6585 (ptt90) outliers start: 32 outliers final: 21 residues processed: 160 average time/residue: 0.1606 time to fit residues: 36.5787 Evaluate side-chains 163 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 63 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.0000 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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: 0.7633 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7824 Z= 0.171 Angle : 0.805 32.304 10622 Z= 0.340 Chirality : 0.038 0.180 1164 Planarity : 0.005 0.066 1272 Dihedral : 15.445 151.452 1142 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.28 % Allowed : 21.21 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.12 (0.29), residues: 894 helix: 1.66 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.81 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 290 HIS 0.002 0.001 HIS B 159 PHE 0.009 0.001 PHE B 105 TYR 0.013 0.001 TYR A 465 ARG 0.004 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 0.886 Fit side-chains REVERT: A 136 MET cc_start: 0.8133 (mmm) cc_final: 0.7842 (mmt) REVERT: A 219 MET cc_start: 0.8261 (tpp) cc_final: 0.7745 (tpp) REVERT: A 250 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7776 (mp) REVERT: A 367 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7851 (tt) REVERT: A 400 MET cc_start: 0.7091 (tpp) cc_final: 0.6796 (tpp) REVERT: A 414 LEU cc_start: 0.8241 (tt) cc_final: 0.7764 (tp) REVERT: A 416 ARG cc_start: 0.7031 (mtt180) cc_final: 0.6655 (ptt90) REVERT: A 417 ASP cc_start: 0.8511 (t0) cc_final: 0.8232 (t0) REVERT: B 219 MET cc_start: 0.8224 (tpp) cc_final: 0.7708 (tpp) REVERT: B 367 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7828 (tt) REVERT: B 416 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6631 (ptt90) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.1692 time to fit residues: 36.9408 Evaluate side-chains 164 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7824 Z= 0.159 Angle : 0.796 32.282 10622 Z= 0.334 Chirality : 0.038 0.167 1164 Planarity : 0.005 0.066 1272 Dihedral : 15.107 146.189 1142 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.41 % Allowed : 22.22 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.24 (0.30), residues: 894 helix: 1.75 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.78 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 461 HIS 0.003 0.001 HIS A 159 PHE 0.009 0.001 PHE B 105 TYR 0.017 0.001 TYR A 269 ARG 0.004 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 0.871 Fit side-chains REVERT: A 219 MET cc_start: 0.8225 (tpp) cc_final: 0.7738 (tpp) REVERT: A 250 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 367 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7823 (tt) REVERT: A 416 ARG cc_start: 0.7005 (mtt180) cc_final: 0.6640 (ptt90) REVERT: A 417 ASP cc_start: 0.8537 (t0) cc_final: 0.8295 (t0) REVERT: B 219 MET cc_start: 0.8187 (tpp) cc_final: 0.7701 (tpp) REVERT: B 367 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 400 MET cc_start: 0.7113 (tpp) cc_final: 0.6785 (tpp) REVERT: B 413 ASN cc_start: 0.7812 (t0) cc_final: 0.7605 (t0) REVERT: B 417 ASP cc_start: 0.8570 (t0) cc_final: 0.8264 (t0) outliers start: 27 outliers final: 18 residues processed: 158 average time/residue: 0.1610 time to fit residues: 36.5030 Evaluate side-chains 162 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7635 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7824 Z= 0.171 Angle : 0.806 32.261 10622 Z= 0.339 Chirality : 0.038 0.161 1164 Planarity : 0.005 0.068 1272 Dihedral : 14.887 143.001 1142 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.66 % Allowed : 23.61 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.25 (0.30), residues: 894 helix: 1.76 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.77 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 461 HIS 0.003 0.001 HIS B 159 PHE 0.008 0.001 PHE B 105 TYR 0.014 0.001 TYR B 465 ARG 0.001 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 0.917 Fit side-chains REVERT: A 136 MET cc_start: 0.8213 (mmm) cc_final: 0.7765 (mmt) REVERT: A 219 MET cc_start: 0.8214 (tpp) cc_final: 0.7735 (tpp) REVERT: A 250 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 400 MET cc_start: 0.7232 (tpp) cc_final: 0.6873 (tpp) REVERT: A 416 ARG cc_start: 0.7002 (mtt180) cc_final: 0.6613 (ptt90) REVERT: A 417 ASP cc_start: 0.8528 (t0) cc_final: 0.8318 (t0) REVERT: B 219 MET cc_start: 0.8173 (tpp) cc_final: 0.7701 (tpp) REVERT: B 367 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7837 (tt) REVERT: B 416 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6708 (ptt90) REVERT: B 417 ASP cc_start: 0.8569 (t0) cc_final: 0.8298 (t0) outliers start: 29 outliers final: 20 residues processed: 159 average time/residue: 0.1546 time to fit residues: 35.2760 Evaluate side-chains 165 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7661 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 7824 Z= 0.192 Angle : 0.824 32.255 10622 Z= 0.347 Chirality : 0.038 0.177 1164 Planarity : 0.005 0.070 1272 Dihedral : 14.740 142.091 1142 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.54 % Allowed : 24.49 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.20 (0.30), residues: 894 helix: 1.73 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.81 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 461 HIS 0.003 0.001 HIS B 159 PHE 0.009 0.001 PHE B 105 TYR 0.018 0.001 TYR A 269 ARG 0.001 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.859 Fit side-chains REVERT: A 136 MET cc_start: 0.8236 (mmm) cc_final: 0.7826 (mmt) REVERT: A 219 MET cc_start: 0.8248 (tpp) cc_final: 0.7734 (tpp) REVERT: A 250 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 400 MET cc_start: 0.7237 (tpp) cc_final: 0.6925 (tpp) REVERT: A 416 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6647 (ptt90) REVERT: B 219 MET cc_start: 0.8204 (tpp) cc_final: 0.7710 (tpp) REVERT: B 250 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 400 MET cc_start: 0.7192 (tpp) cc_final: 0.6790 (tpp) REVERT: B 414 LEU cc_start: 0.8306 (tt) cc_final: 0.8055 (tt) REVERT: B 417 ASP cc_start: 0.8622 (t0) cc_final: 0.8366 (t0) outliers start: 28 outliers final: 22 residues processed: 160 average time/residue: 0.1592 time to fit residues: 36.4520 Evaluate side-chains 168 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7652 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7824 Z= 0.186 Angle : 0.838 32.304 10622 Z= 0.353 Chirality : 0.038 0.179 1164 Planarity : 0.005 0.073 1272 Dihedral : 14.593 139.992 1142 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.90 % Allowed : 25.63 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.21 (0.30), residues: 894 helix: 1.76 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.84 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 461 HIS 0.003 0.001 HIS B 159 PHE 0.008 0.001 PHE B 105 TYR 0.016 0.001 TYR A 465 ARG 0.001 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.873 Fit side-chains REVERT: A 136 MET cc_start: 0.8252 (mmm) cc_final: 0.7860 (mmt) REVERT: A 157 MET cc_start: 0.6698 (ptp) cc_final: 0.6495 (ptt) REVERT: A 219 MET cc_start: 0.8246 (tpp) cc_final: 0.7721 (tpp) REVERT: A 416 ARG cc_start: 0.7033 (mtt180) cc_final: 0.6647 (ptt90) REVERT: B 219 MET cc_start: 0.8217 (tpp) cc_final: 0.7702 (tpp) REVERT: B 400 MET cc_start: 0.7138 (tpp) cc_final: 0.6760 (tpp) REVERT: B 416 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6685 (ptt90) REVERT: B 417 ASP cc_start: 0.8670 (t0) cc_final: 0.8463 (t0) outliers start: 23 outliers final: 20 residues processed: 159 average time/residue: 0.1579 time to fit residues: 35.7990 Evaluate side-chains 165 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7689 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 7824 Z= 0.217 Angle : 0.866 32.262 10622 Z= 0.368 Chirality : 0.039 0.170 1164 Planarity : 0.005 0.075 1272 Dihedral : 14.475 140.376 1142 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.90 % Allowed : 25.38 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.10 (0.29), residues: 894 helix: 1.66 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.86 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 461 HIS 0.004 0.001 HIS B 159 PHE 0.012 0.001 PHE B 476 TYR 0.018 0.001 TYR B 465 ARG 0.002 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 0.894 Fit side-chains REVERT: A 136 MET cc_start: 0.8257 (mmm) cc_final: 0.7858 (mmt) REVERT: A 157 MET cc_start: 0.6911 (ptp) cc_final: 0.6704 (ptt) REVERT: A 219 MET cc_start: 0.8308 (tpp) cc_final: 0.7765 (tpp) REVERT: A 400 MET cc_start: 0.7198 (tpp) cc_final: 0.6731 (tpp) REVERT: A 416 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6674 (ptt90) REVERT: B 157 MET cc_start: 0.6915 (ptp) cc_final: 0.6709 (ptt) REVERT: B 219 MET cc_start: 0.8287 (tpp) cc_final: 0.7741 (tpp) REVERT: B 306 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: B 400 MET cc_start: 0.7141 (tpp) cc_final: 0.6801 (tpp) REVERT: B 416 ARG cc_start: 0.7294 (mtt180) cc_final: 0.6671 (ptt90) outliers start: 23 outliers final: 19 residues processed: 159 average time/residue: 0.1556 time to fit residues: 35.1869 Evaluate side-chains 167 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132170 restraints weight = 10487.517| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.83 r_work: 0.3439 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 7824 Z= 0.189 Angle : 0.865 32.366 10622 Z= 0.369 Chirality : 0.039 0.167 1164 Planarity : 0.005 0.077 1272 Dihedral : 14.274 137.773 1142 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.53 % Allowed : 25.88 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.14 (0.29), residues: 894 helix: 1.71 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -2.87 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 461 HIS 0.003 0.001 HIS A 159 PHE 0.008 0.001 PHE B 105 TYR 0.015 0.001 TYR A 465 ARG 0.012 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1851.21 seconds wall clock time: 34 minutes 13.05 seconds (2053.05 seconds total)