Starting phenix.real_space_refine on Sat Dec 28 05:15:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tel_41190/12_2024/8tel_41190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tel_41190/12_2024/8tel_41190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tel_41190/12_2024/8tel_41190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tel_41190/12_2024/8tel_41190.map" model { file = "/net/cci-nas-00/data/ceres_data/8tel_41190/12_2024/8tel_41190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tel_41190/12_2024/8tel_41190.cif" } resolution = 2.77 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 52 5.16 5 C 5110 2.51 5 N 1290 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7806 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3903 Classifications: {'peptide': 494} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 467} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B Time building chain proxies: 3.74, per 1000 atoms: 0.48 Number of scatterers: 7806 At special positions: 0 Unit cell: (85.49, 120.35, 93.79, 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 52 16.00 P 2 15.00 O 1352 8.00 N 1290 7.00 C 5110 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 2.6 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 77.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.634A pdb=" N ALA A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 62 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.686A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 145 through 151 removed outlier: 4.184A pdb=" N ASN A 149 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.792A pdb=" N GLY A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 251 removed outlier: 6.415A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.377A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.731A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.570A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 391 removed outlier: 3.688A pdb=" N LYS A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.291A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.829A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.634A pdb=" N ALA B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 62 Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 96 through 112 removed outlier: 3.686A pdb=" N ALA B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 142 Processing helix chain 'B' and resid 145 through 151 removed outlier: 4.184A pdb=" N ASN B 149 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 178 removed outlier: 3.792A pdb=" N GLY B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 192 Processing helix chain 'B' and resid 193 through 219 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 228 through 251 removed outlier: 6.415A pdb=" N VAL B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 258 removed outlier: 4.377A pdb=" N GLY B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.732A pdb=" N LEU B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.570A pdb=" N SER B 313 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 359 through 391 removed outlier: 3.688A pdb=" N LYS B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 Processing helix chain 'B' and resid 424 through 431 Processing helix chain 'B' and resid 442 through 446 Processing helix chain 'B' and resid 447 through 453 removed outlier: 4.292A pdb=" N ASP B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 464 through 477 Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.828A pdb=" N LEU B 492 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'B' and resid 93 through 94 522 hydrogen bonds defined for protein. 1506 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: 2.76 Time building geometry restraints manager: 2.44 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: 2420 1.34 - 1.46: 1850 1.46 - 1.58: 3630 1.58 - 1.70: 6 1.70 - 1.82: 90 Bond restraints: 7996 Sorted by residual: bond pdb=" OG1 TPO B 410 " pdb=" P TPO B 410 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3P TPO B 410 " pdb=" P TPO B 410 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O2P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 7991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 10748 2.43 - 4.86: 90 4.86 - 7.29: 4 7.29 - 9.72: 2 9.72 - 12.15: 2 Bond angle restraints: 10846 Sorted by residual: angle pdb=" CB TPO A 410 " pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 119.31 107.16 12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CB TPO B 410 " pdb=" OG1 TPO B 410 " pdb=" P TPO B 410 " ideal model delta sigma weight residual 119.31 107.16 12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N VAL B 413 " pdb=" CA VAL B 413 " pdb=" C VAL B 413 " ideal model delta sigma weight residual 113.53 110.46 3.07 9.80e-01 1.04e+00 9.83e+00 angle pdb=" N VAL A 413 " pdb=" CA VAL A 413 " pdb=" C VAL A 413 " ideal model delta sigma weight residual 113.53 110.48 3.05 9.80e-01 1.04e+00 9.67e+00 angle pdb=" OG1 TPO B 410 " pdb=" P TPO B 410 " pdb=" O1P TPO B 410 " ideal model delta sigma weight residual 100.43 109.76 -9.33 3.00e+00 1.11e-01 9.66e+00 ... (remaining 10841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4030 17.68 - 35.37: 506 35.37 - 53.05: 144 53.05 - 70.73: 38 70.73 - 88.42: 10 Dihedral angle restraints: 4728 sinusoidal: 1892 harmonic: 2836 Sorted by residual: dihedral pdb=" CA ILE B 291 " pdb=" C ILE B 291 " pdb=" N VAL B 292 " pdb=" CA VAL B 292 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ILE A 291 " pdb=" C ILE A 291 " pdb=" N VAL A 292 " pdb=" CA VAL A 292 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CB GLU B 323 " pdb=" CG GLU B 323 " pdb=" CD GLU B 323 " pdb=" OE1 GLU B 323 " ideal model delta sinusoidal sigma weight residual 0.00 -88.42 88.42 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 4725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 863 0.029 - 0.057: 219 0.057 - 0.086: 101 0.086 - 0.114: 38 0.114 - 0.143: 11 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA ILE A 181 " pdb=" N ILE A 181 " pdb=" C ILE A 181 " pdb=" CB ILE A 181 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE B 181 " pdb=" N ILE B 181 " pdb=" C ILE B 181 " pdb=" CB ILE B 181 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1229 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 258 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 259 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 258 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 259 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 226 " 0.009 2.00e-02 2.50e+03 8.01e-03 1.28e+00 pdb=" CG TYR A 226 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 226 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 226 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 226 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 226 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 226 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 226 " 0.000 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 67 2.64 - 3.20: 7220 3.20 - 3.77: 12090 3.77 - 4.33: 16309 4.33 - 4.90: 27518 Nonbonded interactions: 63204 Sorted by model distance: nonbonded pdb=" O PHE A 298 " pdb=" OG SER A 302 " model vdw 2.075 3.040 nonbonded pdb=" O PHE B 298 " pdb=" OG SER B 302 " model vdw 2.075 3.040 nonbonded pdb=" OG SER A 195 " pdb=" OG SER B 195 " model vdw 2.153 3.040 nonbonded pdb=" O LYS A 424 " pdb=" OG1 THR A 427 " model vdw 2.197 3.040 nonbonded pdb=" O LYS B 424 " pdb=" OG1 THR B 427 " model vdw 2.197 3.040 ... (remaining 63199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 13.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.990 Find NCS groups from input model: 0.180 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:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 0.108 7996 Z= 0.225 Angle : 0.551 12.153 10846 Z= 0.264 Chirality : 0.035 0.143 1232 Planarity : 0.003 0.035 1346 Dihedral : 17.767 88.419 2904 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.20 % Allowed : 22.97 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.33 (0.27), residues: 970 helix: 2.14 (0.20), residues: 674 sheet: None (None), residues: 0 loop : 0.22 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 247 HIS 0.002 0.000 HIS B 312 PHE 0.004 0.001 PHE A 192 TYR 0.019 0.001 TYR A 226 ARG 0.002 0.000 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.881 Fit side-chains REVERT: A 226 TYR cc_start: 0.6885 (m-80) cc_final: 0.6522 (m-80) REVERT: B 226 TYR cc_start: 0.6860 (m-80) cc_final: 0.6517 (m-80) outliers start: 10 outliers final: 10 residues processed: 95 average time/residue: 1.3030 time to fit residues: 131.2853 Evaluate side-chains 93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 490 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8298 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7996 Z= 0.172 Angle : 0.477 5.346 10846 Z= 0.243 Chirality : 0.039 0.155 1232 Planarity : 0.004 0.050 1346 Dihedral : 4.865 50.024 1076 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.87 % Allowed : 21.65 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.60 (0.27), residues: 970 helix: 2.39 (0.19), residues: 680 sheet: None (None), residues: 0 loop : 0.15 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.004 0.001 HIS A 312 PHE 0.007 0.001 PHE A 105 TYR 0.014 0.001 TYR B 405 ARG 0.001 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.989 Fit side-chains REVERT: A 35 ARG cc_start: 0.7268 (mtt-85) cc_final: 0.6378 (mpt180) REVERT: A 150 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6946 (mpp80) REVERT: A 226 TYR cc_start: 0.7127 (m-80) cc_final: 0.6893 (m-80) REVERT: A 242 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 20 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7770 (ptp) REVERT: B 35 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.6417 (mpt180) REVERT: B 150 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6898 (mpp80) REVERT: B 226 TYR cc_start: 0.7132 (m-80) cc_final: 0.6893 (m-80) REVERT: B 242 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8359 (tp) outliers start: 24 outliers final: 4 residues processed: 105 average time/residue: 1.4981 time to fit residues: 165.5304 Evaluate side-chains 96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 0.0070 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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: 0.8406 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7996 Z= 0.175 Angle : 0.479 6.513 10846 Z= 0.242 Chirality : 0.039 0.157 1232 Planarity : 0.004 0.048 1346 Dihedral : 3.947 27.879 1064 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.75 % Allowed : 21.29 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.58 (0.26), residues: 970 helix: 2.36 (0.19), residues: 680 sheet: None (None), residues: 0 loop : 0.19 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.003 0.001 HIS A 312 PHE 0.007 0.001 PHE A 498 TYR 0.017 0.001 TYR B 405 ARG 0.002 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.870 Fit side-chains REVERT: A 20 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7665 (ptp) REVERT: A 35 ARG cc_start: 0.7449 (mtt-85) cc_final: 0.6585 (mpt180) REVERT: A 181 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6820 (mt) REVERT: A 242 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8365 (tp) REVERT: A 284 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7242 (mmpt) REVERT: A 390 THR cc_start: 0.6820 (OUTLIER) cc_final: 0.6554 (p) REVERT: A 463 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7524 (pp30) REVERT: B 20 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7680 (ptp) REVERT: B 35 ARG cc_start: 0.7463 (mtt-85) cc_final: 0.6568 (mpt180) REVERT: B 181 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6825 (mt) REVERT: B 242 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8369 (tp) REVERT: B 284 LYS cc_start: 0.7687 (mmtt) cc_final: 0.7224 (mmpt) REVERT: B 463 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7438 (pp30) outliers start: 23 outliers final: 7 residues processed: 103 average time/residue: 1.4136 time to fit residues: 153.5633 Evaluate side-chains 101 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 0.0070 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- 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: 0.8448 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7996 Z= 0.226 Angle : 0.519 6.211 10846 Z= 0.263 Chirality : 0.040 0.167 1232 Planarity : 0.004 0.046 1346 Dihedral : 4.115 22.311 1064 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.71 % Allowed : 20.93 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.26 (0.26), residues: 970 helix: 2.13 (0.19), residues: 682 sheet: None (None), residues: 0 loop : 0.01 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.004 0.001 HIS A 312 PHE 0.007 0.001 PHE B 498 TYR 0.009 0.001 TYR B 495 ARG 0.002 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.884 Fit side-chains REVERT: A 20 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7737 (ptp) REVERT: A 135 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8195 (mtt) REVERT: A 242 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8376 (tp) REVERT: A 284 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7183 (mmpt) REVERT: A 463 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.7551 (pp30) REVERT: B 135 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8200 (mtt) REVERT: B 242 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8405 (tp) REVERT: B 284 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7184 (mmpt) REVERT: B 463 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7535 (pp30) outliers start: 31 outliers final: 8 residues processed: 102 average time/residue: 1.3198 time to fit residues: 142.3832 Evaluate side-chains 93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8417 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7996 Z= 0.160 Angle : 0.466 6.635 10846 Z= 0.235 Chirality : 0.038 0.153 1232 Planarity : 0.004 0.047 1346 Dihedral : 3.851 18.345 1062 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.23 % Allowed : 21.05 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.41 (0.26), residues: 970 helix: 2.26 (0.19), residues: 680 sheet: None (None), residues: 0 loop : 0.03 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.006 0.001 PHE A 498 TYR 0.021 0.001 TYR A 405 ARG 0.001 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.963 Fit side-chains REVERT: A 20 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7635 (ptp) REVERT: A 30 PHE cc_start: 0.7914 (m-80) cc_final: 0.7661 (m-80) REVERT: A 135 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: A 150 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6894 (mpp80) REVERT: A 284 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7171 (mmpt) REVERT: A 463 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7465 (pp30) REVERT: B 20 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7650 (ptp) REVERT: B 30 PHE cc_start: 0.7927 (m-80) cc_final: 0.7667 (m-80) REVERT: B 135 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: B 150 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6908 (mpp80) REVERT: B 217 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7049 (mtt90) REVERT: B 284 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7172 (mmpt) outliers start: 27 outliers final: 6 residues processed: 97 average time/residue: 1.5293 time to fit residues: 156.6217 Evaluate side-chains 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 0.0060 chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.8392 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7996 Z= 0.139 Angle : 0.443 5.364 10846 Z= 0.224 Chirality : 0.037 0.151 1232 Planarity : 0.004 0.048 1346 Dihedral : 3.720 16.819 1062 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.83 % Allowed : 20.93 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.61 (0.27), residues: 970 helix: 2.38 (0.19), residues: 680 sheet: None (None), residues: 0 loop : 0.18 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.006 0.001 PHE B 498 TYR 0.007 0.001 TYR B 495 ARG 0.001 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.904 Fit side-chains REVERT: A 150 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6931 (mpp80) REVERT: A 217 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7033 (mtt90) REVERT: A 242 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8350 (tp) REVERT: A 284 LYS cc_start: 0.7616 (mmtt) cc_final: 0.7154 (mmpt) REVERT: A 406 HIS cc_start: 0.6594 (m90) cc_final: 0.6061 (t70) REVERT: B 20 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7525 (ptp) REVERT: B 150 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6914 (mpp80) REVERT: B 242 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8345 (tp) REVERT: B 284 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7154 (mmpt) REVERT: B 406 HIS cc_start: 0.6601 (m90) cc_final: 0.6063 (t70) REVERT: B 463 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7464 (pp30) outliers start: 32 outliers final: 6 residues processed: 101 average time/residue: 1.3644 time to fit residues: 145.7574 Evaluate side-chains 96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 94 optimal weight: 0.0070 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7996 Z= 0.139 Angle : 0.454 8.390 10846 Z= 0.225 Chirality : 0.038 0.149 1232 Planarity : 0.004 0.050 1346 Dihedral : 3.683 17.227 1062 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.99 % Allowed : 22.13 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.68 (0.26), residues: 970 helix: 2.42 (0.19), residues: 680 sheet: None (None), residues: 0 loop : 0.26 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.006 0.001 PHE B 30 TYR 0.022 0.001 TYR B 405 ARG 0.001 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.942 Fit side-chains REVERT: A 135 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: A 150 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6940 (mpp80) REVERT: A 217 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6948 (mtt90) REVERT: A 242 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 284 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7163 (mmpt) REVERT: A 406 HIS cc_start: 0.6605 (m90) cc_final: 0.6102 (t70) REVERT: A 463 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7458 (pp30) REVERT: B 20 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7585 (ptp) REVERT: B 135 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8254 (mtt) REVERT: B 150 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6892 (mpp80) REVERT: B 217 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6981 (mtt90) REVERT: B 242 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8347 (tp) REVERT: B 284 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7165 (mmpt) REVERT: B 406 HIS cc_start: 0.6612 (m90) cc_final: 0.6107 (t70) REVERT: B 463 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7478 (pp30) outliers start: 25 outliers final: 10 residues processed: 96 average time/residue: 1.4387 time to fit residues: 145.8099 Evaluate side-chains 104 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.0470 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 74 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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: 0.8374 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7996 Z= 0.133 Angle : 0.443 7.105 10846 Z= 0.221 Chirality : 0.037 0.148 1232 Planarity : 0.004 0.050 1346 Dihedral : 3.665 17.270 1062 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.51 % Allowed : 22.73 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.76 (0.27), residues: 970 helix: 2.41 (0.19), residues: 694 sheet: None (None), residues: 0 loop : 0.37 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.005 0.001 PHE A 498 TYR 0.007 0.001 TYR A 42 ARG 0.001 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.007 Fit side-chains REVERT: A 135 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8259 (mtt) REVERT: A 150 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6875 (mtp85) REVERT: A 217 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6961 (mtt90) REVERT: A 242 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8344 (tp) REVERT: A 284 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7153 (mmpt) REVERT: A 406 HIS cc_start: 0.6554 (m90) cc_final: 0.6117 (t70) REVERT: A 463 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7437 (pp30) REVERT: B 20 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7569 (ptp) REVERT: B 135 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8259 (mtt) REVERT: B 150 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6878 (mtp85) REVERT: B 217 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6980 (mtt90) REVERT: B 242 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8340 (tp) REVERT: B 284 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7144 (mmpt) REVERT: B 406 HIS cc_start: 0.6562 (m90) cc_final: 0.6123 (t70) REVERT: B 463 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7460 (pp30) outliers start: 21 outliers final: 8 residues processed: 94 average time/residue: 1.4717 time to fit residues: 145.9140 Evaluate side-chains 103 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7996 Z= 0.137 Angle : 0.444 6.689 10846 Z= 0.222 Chirality : 0.038 0.148 1232 Planarity : 0.004 0.051 1346 Dihedral : 3.645 16.364 1062 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.87 % Allowed : 22.49 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.78 (0.27), residues: 970 helix: 2.43 (0.19), residues: 692 sheet: None (None), residues: 0 loop : 0.38 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS B 312 PHE 0.005 0.001 PHE B 498 TYR 0.024 0.001 TYR B 405 ARG 0.001 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.129 Fit side-chains REVERT: A 135 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: A 150 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6865 (mtp85) REVERT: A 217 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6944 (mtt90) REVERT: A 242 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8357 (tp) REVERT: A 284 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7160 (mmpt) REVERT: A 406 HIS cc_start: 0.6573 (m90) cc_final: 0.6109 (t70) REVERT: A 463 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7473 (pp30) REVERT: B 20 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7587 (ptp) REVERT: B 135 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8271 (mtt) REVERT: B 150 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6879 (mtp85) REVERT: B 217 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6955 (mtt90) REVERT: B 242 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8354 (tp) REVERT: B 284 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7153 (mmpt) REVERT: B 406 HIS cc_start: 0.6580 (m90) cc_final: 0.6115 (t70) REVERT: B 463 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7495 (pp30) outliers start: 24 outliers final: 10 residues processed: 97 average time/residue: 1.4853 time to fit residues: 151.7518 Evaluate side-chains 106 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.0042 ------------------------------------------------------------------------------- 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: 0.8412 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7996 Z= 0.169 Angle : 0.474 6.182 10846 Z= 0.238 Chirality : 0.039 0.153 1232 Planarity : 0.004 0.050 1346 Dihedral : 3.774 16.277 1062 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.63 % Allowed : 22.97 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.59 (0.27), residues: 970 helix: 2.29 (0.19), residues: 692 sheet: None (None), residues: 0 loop : 0.31 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 131 HIS 0.003 0.001 HIS B 312 PHE 0.006 0.001 PHE A 179 TYR 0.024 0.001 TYR B 405 ARG 0.002 0.000 ARG B 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.927 Fit side-chains REVERT: A 135 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8229 (mtt) REVERT: A 150 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6867 (mtp85) REVERT: A 217 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6977 (mtt90) REVERT: A 242 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 284 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7152 (mmpt) REVERT: A 406 HIS cc_start: 0.6604 (m90) cc_final: 0.6066 (t70) REVERT: A 463 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7489 (pp30) REVERT: B 20 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7584 (ptp) REVERT: B 135 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: B 150 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6896 (mpp80) REVERT: B 217 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6971 (mtt90) REVERT: B 242 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8398 (tp) REVERT: B 284 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7164 (mmpt) REVERT: B 406 HIS cc_start: 0.6596 (m90) cc_final: 0.6065 (t70) REVERT: B 463 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7431 (pp30) outliers start: 22 outliers final: 9 residues processed: 97 average time/residue: 1.4512 time to fit residues: 148.2704 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 499 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.154873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113285 restraints weight = 8715.289| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.72 r_work: 0.3039 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7996 Z= 0.140 Angle : 0.452 6.214 10846 Z= 0.227 Chirality : 0.038 0.149 1232 Planarity : 0.004 0.052 1346 Dihedral : 3.693 16.821 1062 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.51 % Allowed : 23.09 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.77 (0.27), residues: 970 helix: 2.43 (0.19), residues: 692 sheet: None (None), residues: 0 loop : 0.37 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.005 0.001 PHE A 498 TYR 0.024 0.001 TYR B 405 ARG 0.001 0.000 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.58 seconds wall clock time: 56 minutes 3.15 seconds (3363.15 seconds total)