Starting phenix.real_space_refine on Wed Feb 14 23:27:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghc_40040/02_2024/8ghc_40040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghc_40040/02_2024/8ghc_40040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghc_40040/02_2024/8ghc_40040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghc_40040/02_2024/8ghc_40040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghc_40040/02_2024/8ghc_40040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghc_40040/02_2024/8ghc_40040_updated.pdb" } resolution = 2.3 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= 0.004 sd= 1.385 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 Fe 2 7.16 5 S 67 5.16 5 C 6714 2.51 5 N 1830 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10512 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "B" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5193 Classifications: {'peptide': 648} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 606} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.96, per 1000 atoms: 0.57 Number of scatterers: 10512 At special positions: 0 Unit cell: (67.24, 121.36, 131.2, 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) Fe 2 26.01 S 67 16.00 O 1899 8.00 N 1830 7.00 C 6714 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: 4.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 9 sheets defined 41.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.675A pdb=" N GLN A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 168 through 193 Processing helix chain 'A' and resid 200 through 206 removed outlier: 3.588A pdb=" N ILE A 206 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.144A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 384 through 393 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 414 through 417 No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 459 through 482 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 584 through 598 Processing helix chain 'A' and resid 618 through 644 removed outlier: 4.135A pdb=" N GLN A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.555A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 4.355A pdb=" N GLY B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 203 removed outlier: 3.806A pdb=" N PHE B 203 " --> pdb=" O LEU B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.080A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 337 through 356 Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.951A pdb=" N ALA B 448 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 482 removed outlier: 3.787A pdb=" N LEU B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 490 Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 510 through 513 Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 538 through 547 removed outlier: 4.618A pdb=" N GLY B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLN B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 574 through 580 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 618 through 642 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 52 removed outlier: 4.270A pdb=" N TRP A 76 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= C, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.547A pdb=" N ASN A 20 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 21 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 80 through 83 Processing sheet with id= E, first strand: chain 'A' and resid 273 through 277 removed outlier: 3.640A pdb=" N VAL A 315 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS A 304 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.383A pdb=" N TRP B 76 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.410A pdb=" N ARG B 21 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 80 through 83 Processing sheet with id= I, first strand: chain 'B' and resid 273 through 277 removed outlier: 5.666A pdb=" N LYS B 304 " --> pdb=" O PRO B 313 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1248 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: 3.82 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2049 1.32 - 1.45: 2673 1.45 - 1.57: 5965 1.57 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 10787 Sorted by residual: bond pdb=" CB VAL B 584 " pdb=" CG1 VAL B 584 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.45e+00 bond pdb=" CB ILE B 413 " pdb=" CG2 ILE B 413 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.71e+00 bond pdb=" CG LEU B 362 " pdb=" CD2 LEU B 362 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.00e+00 bond pdb=" CG LEU A 240 " pdb=" CD2 LEU A 240 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.21e+00 bond pdb=" CB VAL B 92 " pdb=" CG1 VAL B 92 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 4.98e+00 ... (remaining 10782 not shown) Histogram of bond angle deviations from ideal: 97.64 - 105.26: 290 105.26 - 112.89: 5659 112.89 - 120.51: 4667 120.51 - 128.14: 3893 128.14 - 135.77: 154 Bond angle restraints: 14663 Sorted by residual: angle pdb=" N PRO B 443 " pdb=" CA PRO B 443 " pdb=" C PRO B 443 " ideal model delta sigma weight residual 110.70 115.61 -4.91 1.22e+00 6.72e-01 1.62e+01 angle pdb=" N PRO A 443 " pdb=" CA PRO A 443 " pdb=" C PRO A 443 " ideal model delta sigma weight residual 110.70 115.41 -4.71 1.22e+00 6.72e-01 1.49e+01 angle pdb=" CA PRO B 443 " pdb=" C PRO B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 117.93 122.39 -4.46 1.20e+00 6.94e-01 1.38e+01 angle pdb=" CA PRO A 443 " pdb=" C PRO A 443 " pdb=" N PRO A 444 " ideal model delta sigma weight residual 117.93 122.31 -4.38 1.20e+00 6.94e-01 1.33e+01 angle pdb=" CA PRO A 391 " pdb=" N PRO A 391 " pdb=" CD PRO A 391 " ideal model delta sigma weight residual 112.00 106.92 5.08 1.40e+00 5.10e-01 1.32e+01 ... (remaining 14658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5955 17.34 - 34.67: 418 34.67 - 52.01: 67 52.01 - 69.35: 28 69.35 - 86.68: 8 Dihedral angle restraints: 6476 sinusoidal: 2671 harmonic: 3805 Sorted by residual: dihedral pdb=" CA ASP A 335 " pdb=" C ASP A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ALA A 417 " pdb=" C ALA A 417 " pdb=" N VAL A 418 " pdb=" CA VAL A 418 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ALA B 417 " pdb=" C ALA B 417 " pdb=" N VAL B 418 " pdb=" CA VAL B 418 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1173 0.062 - 0.124: 346 0.124 - 0.185: 52 0.185 - 0.247: 8 0.247 - 0.309: 4 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CG LEU B 362 " pdb=" CB LEU B 362 " pdb=" CD1 LEU B 362 " pdb=" CD2 LEU B 362 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB THR B 327 " pdb=" CA THR B 327 " pdb=" OG1 THR B 327 " pdb=" CG2 THR B 327 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CG LEU B 240 " pdb=" CB LEU B 240 " pdb=" CD1 LEU B 240 " pdb=" CD2 LEU B 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1580 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 94 " -0.020 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C PHE B 94 " 0.067 2.00e-02 2.50e+03 pdb=" O PHE B 94 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 95 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 197 " 0.005 2.00e-02 2.50e+03 2.30e-02 1.33e+01 pdb=" CG TRP B 197 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 197 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP B 197 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 197 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP B 197 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 197 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 197 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 197 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 197 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 349 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CG ASN A 349 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A 349 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 349 " -0.019 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 154 2.63 - 3.20: 9080 3.20 - 3.77: 18755 3.77 - 4.33: 25794 4.33 - 4.90: 40879 Nonbonded interactions: 94662 Sorted by model distance: nonbonded pdb=" OXT ILE B 663 " pdb="FE FE2 B 901 " model vdw 2.067 3.000 nonbonded pdb=" NE2 HIS B 360 " pdb="FE FE2 B 901 " model vdw 2.099 3.080 nonbonded pdb=" NE2 HIS A 365 " pdb="FE FE2 A 901 " model vdw 2.131 3.080 nonbonded pdb=" NE2 HIS B 540 " pdb="FE FE2 B 901 " model vdw 2.131 3.080 nonbonded pdb=" NE2 HIS A 360 " pdb="FE FE2 A 901 " model vdw 2.131 3.080 ... (remaining 94657 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' and (resid 2 through 155 or resid 170 through 663 or resid 901)) 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.320 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.730 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.200 ------------------------------------------------------------------------------- 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 : 0.009 0.115 10787 Z= 0.621 Angle : 0.907 10.765 14663 Z= 0.478 Chirality : 0.060 0.309 1583 Planarity : 0.008 0.068 1906 Dihedral : 12.960 86.684 4012 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.20), residues: 1304 helix: -1.14 (0.18), residues: 578 sheet: -0.50 (0.42), residues: 128 loop : -0.65 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP B 197 HIS 0.014 0.003 HIS A 480 PHE 0.021 0.004 PHE A 278 TYR 0.023 0.003 TYR A 359 ARG 0.013 0.002 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7526 (tpp-160) cc_final: 0.7212 (tpp-160) REVERT: A 7 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7649 (mtt90) REVERT: A 169 GLU cc_start: 0.7886 (pm20) cc_final: 0.7221 (pm20) REVERT: A 184 GLU cc_start: 0.8182 (tt0) cc_final: 0.7973 (tt0) REVERT: A 394 ARG cc_start: 0.8108 (ptm-80) cc_final: 0.7865 (ppt170) REVERT: A 571 ASP cc_start: 0.7948 (m-30) cc_final: 0.7675 (m-30) REVERT: A 621 LYS cc_start: 0.7934 (mttm) cc_final: 0.7636 (ttpt) REVERT: B 84 GLN cc_start: 0.7882 (tt0) cc_final: 0.7286 (mm-40) REVERT: B 216 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6924 (mm-30) REVERT: B 239 MET cc_start: 0.8980 (mmm) cc_final: 0.8724 (mmm) REVERT: B 305 MET cc_start: 0.8630 (tpt) cc_final: 0.8305 (tpp) REVERT: B 394 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7391 (ttm-80) REVERT: B 568 THR cc_start: 0.8340 (p) cc_final: 0.8114 (p) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 1.4842 time to fit residues: 280.9374 Evaluate side-chains 141 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 GLN B 406 GLN B 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10787 Z= 0.193 Angle : 0.529 7.413 14663 Z= 0.269 Chirality : 0.040 0.144 1583 Planarity : 0.005 0.055 1906 Dihedral : 4.342 19.762 1425 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.33 % Allowed : 8.16 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.22), residues: 1304 helix: 0.10 (0.21), residues: 573 sheet: -0.40 (0.42), residues: 134 loop : -0.21 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 25 HIS 0.006 0.001 HIS B 360 PHE 0.013 0.001 PHE A 386 TYR 0.016 0.002 TYR A 460 ARG 0.007 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.240 Fit side-chains REVERT: A 5 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7319 (tpp-160) REVERT: A 7 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7755 (mtt90) REVERT: A 169 GLU cc_start: 0.7846 (pm20) cc_final: 0.7208 (pm20) REVERT: A 184 GLU cc_start: 0.8144 (tt0) cc_final: 0.7944 (tt0) REVERT: A 621 LYS cc_start: 0.7810 (mttm) cc_final: 0.7547 (ttpt) REVERT: B 7 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7112 (mtt90) REVERT: B 216 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 239 MET cc_start: 0.8866 (mmm) cc_final: 0.8650 (mmm) REVERT: B 305 MET cc_start: 0.8615 (tpt) cc_final: 0.8323 (tpp) REVERT: B 394 ARG cc_start: 0.7757 (ttp-110) cc_final: 0.7333 (ttm-80) REVERT: B 406 GLN cc_start: 0.8407 (mt0) cc_final: 0.8088 (mt0) outliers start: 15 outliers final: 9 residues processed: 156 average time/residue: 1.5403 time to fit residues: 255.5052 Evaluate side-chains 146 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10787 Z= 0.316 Angle : 0.567 7.294 14663 Z= 0.287 Chirality : 0.042 0.165 1583 Planarity : 0.005 0.046 1906 Dihedral : 4.399 20.458 1425 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.39 % Allowed : 9.57 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.22), residues: 1304 helix: 0.49 (0.21), residues: 578 sheet: -0.21 (0.41), residues: 140 loop : -0.14 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 498 HIS 0.006 0.001 HIS A 609 PHE 0.017 0.002 PHE A 386 TYR 0.020 0.002 TYR B 460 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7489 (ttp-110) REVERT: A 169 GLU cc_start: 0.7871 (pm20) cc_final: 0.7232 (pm20) REVERT: A 621 LYS cc_start: 0.7860 (mttm) cc_final: 0.7577 (ttpt) REVERT: B 38 GLN cc_start: 0.8096 (mp10) cc_final: 0.7729 (mm-40) REVERT: B 91 GLU cc_start: 0.7544 (pt0) cc_final: 0.6947 (mt-10) REVERT: B 92 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7865 (p) REVERT: B 216 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 226 GLU cc_start: 0.8044 (pt0) cc_final: 0.7184 (pm20) REVERT: B 249 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8487 (t) REVERT: B 305 MET cc_start: 0.8587 (tpt) cc_final: 0.8295 (tpp) REVERT: B 394 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7321 (ttm-80) REVERT: B 406 GLN cc_start: 0.8415 (mt0) cc_final: 0.8017 (mt0) outliers start: 27 outliers final: 12 residues processed: 152 average time/residue: 1.5492 time to fit residues: 250.4485 Evaluate side-chains 150 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN B 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10787 Z= 0.161 Angle : 0.490 7.057 14663 Z= 0.246 Chirality : 0.039 0.142 1583 Planarity : 0.004 0.041 1906 Dihedral : 4.096 19.661 1425 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.13 % Allowed : 10.73 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.22), residues: 1304 helix: 0.96 (0.21), residues: 571 sheet: -0.09 (0.41), residues: 140 loop : -0.02 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.003 0.001 HIS A 127 PHE 0.010 0.001 PHE A 482 TYR 0.013 0.001 TYR A 460 ARG 0.006 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7740 (mtt90) REVERT: A 48 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: A 66 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7422 (ttp-110) REVERT: A 169 GLU cc_start: 0.7802 (pm20) cc_final: 0.7213 (pm20) REVERT: A 621 LYS cc_start: 0.7798 (mttm) cc_final: 0.7536 (ttpt) REVERT: B 21 ARG cc_start: 0.7843 (mpp80) cc_final: 0.7595 (mtm-85) REVERT: B 34 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: B 38 GLN cc_start: 0.8022 (mp10) cc_final: 0.7646 (mm-40) REVERT: B 91 GLU cc_start: 0.7769 (pt0) cc_final: 0.6879 (mt-10) REVERT: B 92 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7908 (p) REVERT: B 123 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7507 (mmm) REVERT: B 216 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 226 GLU cc_start: 0.7993 (pt0) cc_final: 0.7126 (pm20) REVERT: B 249 SER cc_start: 0.8732 (m) cc_final: 0.8454 (t) REVERT: B 305 MET cc_start: 0.8562 (tpt) cc_final: 0.8291 (tpp) REVERT: B 360 HIS cc_start: 0.8791 (t-170) cc_final: 0.8374 (t-170) REVERT: B 394 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7331 (ttm-80) REVERT: B 406 GLN cc_start: 0.8389 (mt0) cc_final: 0.7985 (mt0) outliers start: 24 outliers final: 7 residues processed: 157 average time/residue: 1.4671 time to fit residues: 245.2755 Evaluate side-chains 148 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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: 0.8330 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10787 Z= 0.225 Angle : 0.512 7.047 14663 Z= 0.257 Chirality : 0.040 0.161 1583 Planarity : 0.004 0.042 1906 Dihedral : 4.120 18.934 1425 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.84 % Allowed : 10.82 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.22), residues: 1304 helix: 1.05 (0.21), residues: 578 sheet: 0.02 (0.41), residues: 140 loop : 0.03 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 498 HIS 0.004 0.001 HIS B 360 PHE 0.012 0.001 PHE A 386 TYR 0.016 0.002 TYR B 460 ARG 0.007 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7685 (tpp-160) cc_final: 0.7233 (ttm-80) REVERT: A 7 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7721 (mtt90) REVERT: A 48 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: A 66 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7416 (ttp-110) REVERT: A 169 GLU cc_start: 0.7810 (pm20) cc_final: 0.7181 (pm20) REVERT: A 593 ILE cc_start: 0.8869 (mm) cc_final: 0.8498 (mt) REVERT: A 621 LYS cc_start: 0.7791 (mttm) cc_final: 0.7541 (ttpt) REVERT: B 7 ARG cc_start: 0.6757 (mtm110) cc_final: 0.6255 (mtt90) REVERT: B 34 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: B 216 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 226 GLU cc_start: 0.7962 (pt0) cc_final: 0.7047 (pm20) REVERT: B 249 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8457 (t) REVERT: B 305 MET cc_start: 0.8555 (tpt) cc_final: 0.8019 (tpp) REVERT: B 360 HIS cc_start: 0.8791 (t-170) cc_final: 0.8476 (t-170) REVERT: B 394 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7287 (ttm-80) REVERT: B 406 GLN cc_start: 0.8393 (mt0) cc_final: 0.8019 (mt0) REVERT: B 595 TRP cc_start: 0.8080 (t60) cc_final: 0.7876 (t60) outliers start: 32 outliers final: 13 residues processed: 156 average time/residue: 1.5539 time to fit residues: 258.4017 Evaluate side-chains 158 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10787 Z= 0.367 Angle : 0.583 7.864 14663 Z= 0.294 Chirality : 0.044 0.225 1583 Planarity : 0.005 0.047 1906 Dihedral : 4.421 19.529 1425 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.39 % Allowed : 11.70 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.22), residues: 1304 helix: 0.83 (0.21), residues: 579 sheet: 0.06 (0.40), residues: 140 loop : 0.04 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 197 HIS 0.006 0.001 HIS A 609 PHE 0.018 0.002 PHE A 386 TYR 0.020 0.002 TYR B 460 ARG 0.008 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7653 (tpp-160) cc_final: 0.6980 (ttm-80) REVERT: A 47 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 48 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: A 66 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7498 (ttp-110) REVERT: A 169 GLU cc_start: 0.7851 (pm20) cc_final: 0.7216 (pm20) REVERT: A 593 ILE cc_start: 0.8840 (mm) cc_final: 0.8542 (mt) REVERT: A 621 LYS cc_start: 0.7816 (mttm) cc_final: 0.7549 (ttpt) REVERT: B 7 ARG cc_start: 0.6904 (mtm110) cc_final: 0.6488 (mtt90) REVERT: B 34 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: B 38 GLN cc_start: 0.8097 (mp10) cc_final: 0.7689 (mm-40) REVERT: B 216 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 226 GLU cc_start: 0.8003 (pt0) cc_final: 0.7154 (pm20) REVERT: B 249 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (t) REVERT: B 305 MET cc_start: 0.8579 (tpt) cc_final: 0.8282 (tpp) REVERT: B 394 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7259 (ttm-80) REVERT: B 406 GLN cc_start: 0.8414 (mt0) cc_final: 0.8066 (mt0) outliers start: 27 outliers final: 14 residues processed: 159 average time/residue: 1.5798 time to fit residues: 267.6308 Evaluate side-chains 160 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 91 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10787 Z= 0.153 Angle : 0.493 8.174 14663 Z= 0.248 Chirality : 0.039 0.169 1583 Planarity : 0.004 0.041 1906 Dihedral : 4.082 18.814 1425 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.68 % Allowed : 12.77 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.22), residues: 1304 helix: 1.22 (0.21), residues: 579 sheet: 0.11 (0.41), residues: 140 loop : 0.09 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 176 HIS 0.004 0.001 HIS B 360 PHE 0.009 0.001 PHE A 482 TYR 0.013 0.001 TYR A 474 ARG 0.006 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.275 Fit side-chains REVERT: A 5 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7253 (ttm-80) REVERT: A 7 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7573 (mtt90) REVERT: A 47 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7387 (mt-10) REVERT: A 66 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7400 (ttp-110) REVERT: A 169 GLU cc_start: 0.7806 (pm20) cc_final: 0.7181 (pm20) REVERT: A 184 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: A 593 ILE cc_start: 0.8873 (mm) cc_final: 0.8591 (mt) REVERT: A 621 LYS cc_start: 0.7767 (mttm) cc_final: 0.7503 (ttpt) REVERT: B 7 ARG cc_start: 0.6969 (mtm110) cc_final: 0.6430 (mtt90) REVERT: B 34 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: B 38 GLN cc_start: 0.7958 (mp10) cc_final: 0.7573 (mm-40) REVERT: B 216 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 249 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8461 (t) REVERT: B 305 MET cc_start: 0.8550 (tpt) cc_final: 0.8059 (tpp) REVERT: B 360 HIS cc_start: 0.8703 (t-90) cc_final: 0.8498 (t-170) REVERT: B 394 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7233 (ttm-80) REVERT: B 406 GLN cc_start: 0.8360 (mt0) cc_final: 0.7985 (mt0) outliers start: 19 outliers final: 9 residues processed: 160 average time/residue: 1.5609 time to fit residues: 265.8006 Evaluate side-chains 162 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10787 Z= 0.236 Angle : 0.526 8.939 14663 Z= 0.262 Chirality : 0.041 0.178 1583 Planarity : 0.004 0.043 1906 Dihedral : 4.139 18.369 1425 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.22 % Allowed : 12.59 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.22), residues: 1304 helix: 1.23 (0.21), residues: 579 sheet: 0.12 (0.40), residues: 140 loop : 0.10 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 176 HIS 0.005 0.001 HIS B 360 PHE 0.011 0.001 PHE A 386 TYR 0.016 0.002 TYR B 460 ARG 0.008 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.349 Fit side-chains REVERT: A 5 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7307 (ttm-80) REVERT: A 47 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7408 (mt-10) REVERT: A 51 HIS cc_start: 0.5991 (m-70) cc_final: 0.5665 (m-70) REVERT: A 66 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7398 (ttp-110) REVERT: A 169 GLU cc_start: 0.7825 (pm20) cc_final: 0.7209 (pm20) REVERT: A 593 ILE cc_start: 0.8887 (mm) cc_final: 0.8600 (mt) REVERT: A 621 LYS cc_start: 0.7784 (mttm) cc_final: 0.7519 (ttpt) REVERT: B 7 ARG cc_start: 0.7025 (mtm110) cc_final: 0.6348 (mtt90) REVERT: B 34 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7416 (tp30) REVERT: B 38 GLN cc_start: 0.7925 (mp10) cc_final: 0.7373 (mm-40) REVERT: B 91 GLU cc_start: 0.7943 (pt0) cc_final: 0.7237 (tt0) REVERT: B 189 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6848 (ttp80) REVERT: B 216 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7180 (mm-30) REVERT: B 226 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: B 249 SER cc_start: 0.8738 (m) cc_final: 0.8473 (t) REVERT: B 305 MET cc_start: 0.8560 (tpt) cc_final: 0.8274 (tpp) REVERT: B 394 ARG cc_start: 0.7805 (ttp-110) cc_final: 0.7242 (ttm-80) REVERT: B 406 GLN cc_start: 0.8376 (mt0) cc_final: 0.8005 (mt0) outliers start: 25 outliers final: 15 residues processed: 159 average time/residue: 1.5190 time to fit residues: 257.2449 Evaluate side-chains 164 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10787 Z= 0.195 Angle : 0.519 9.530 14663 Z= 0.257 Chirality : 0.040 0.181 1583 Planarity : 0.004 0.043 1906 Dihedral : 4.079 17.999 1425 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.86 % Allowed : 12.59 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.22), residues: 1304 helix: 1.31 (0.21), residues: 583 sheet: 0.10 (0.40), residues: 140 loop : 0.14 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 176 HIS 0.005 0.001 HIS B 360 PHE 0.010 0.001 PHE A 482 TYR 0.014 0.001 TYR B 460 ARG 0.008 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.324 Fit side-chains REVERT: A 5 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7259 (ttm-80) REVERT: A 47 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 48 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: A 51 HIS cc_start: 0.5873 (m-70) cc_final: 0.5592 (m-70) REVERT: A 66 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7399 (ttp-110) REVERT: A 169 GLU cc_start: 0.7808 (pm20) cc_final: 0.7199 (pm20) REVERT: A 184 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: A 593 ILE cc_start: 0.8890 (mm) cc_final: 0.8612 (mt) REVERT: A 621 LYS cc_start: 0.7779 (mttm) cc_final: 0.7509 (ttpt) REVERT: B 7 ARG cc_start: 0.7004 (mtm110) cc_final: 0.6467 (mtt90) REVERT: B 34 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: B 38 GLN cc_start: 0.7870 (mp10) cc_final: 0.7540 (mm-40) REVERT: B 91 GLU cc_start: 0.8010 (pt0) cc_final: 0.7599 (tt0) REVERT: B 216 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7145 (mm-30) REVERT: B 249 SER cc_start: 0.8732 (m) cc_final: 0.8469 (t) REVERT: B 305 MET cc_start: 0.8548 (tpt) cc_final: 0.8269 (tpp) REVERT: B 394 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7241 (ttm-80) REVERT: B 406 GLN cc_start: 0.8380 (mt0) cc_final: 0.8003 (mt0) outliers start: 21 outliers final: 12 residues processed: 159 average time/residue: 1.5086 time to fit residues: 256.1160 Evaluate side-chains 164 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10787 Z= 0.225 Angle : 0.539 11.727 14663 Z= 0.265 Chirality : 0.041 0.173 1583 Planarity : 0.004 0.043 1906 Dihedral : 4.121 17.834 1425 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.86 % Allowed : 12.68 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.22), residues: 1304 helix: 1.28 (0.21), residues: 584 sheet: 0.13 (0.40), residues: 140 loop : 0.17 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 176 HIS 0.005 0.001 HIS B 360 PHE 0.011 0.001 PHE A 386 TYR 0.016 0.002 TYR B 460 ARG 0.008 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.239 Fit side-chains REVERT: A 5 ARG cc_start: 0.7572 (tpp-160) cc_final: 0.7200 (ttm-80) REVERT: A 47 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 48 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: A 66 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7395 (ttp-110) REVERT: A 169 GLU cc_start: 0.7816 (pm20) cc_final: 0.7204 (pm20) REVERT: A 593 ILE cc_start: 0.8899 (mm) cc_final: 0.8634 (mt) REVERT: A 621 LYS cc_start: 0.7760 (mttm) cc_final: 0.7499 (ttpt) REVERT: B 7 ARG cc_start: 0.7007 (mtm110) cc_final: 0.6326 (mtt90) REVERT: B 34 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: B 38 GLN cc_start: 0.7832 (mp10) cc_final: 0.7443 (mm-40) REVERT: B 91 GLU cc_start: 0.8048 (pt0) cc_final: 0.7296 (tt0) REVERT: B 216 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7087 (mm-30) REVERT: B 249 SER cc_start: 0.8737 (m) cc_final: 0.8474 (t) REVERT: B 305 MET cc_start: 0.8552 (tpt) cc_final: 0.8271 (tpp) REVERT: B 394 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7217 (ttm-80) REVERT: B 406 GLN cc_start: 0.8381 (mt0) cc_final: 0.8027 (mt0) outliers start: 21 outliers final: 15 residues processed: 160 average time/residue: 1.4284 time to fit residues: 244.2945 Evaluate side-chains 165 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101237 restraints weight = 12846.920| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.08 r_work: 0.3207 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10787 Z= 0.224 Angle : 0.544 12.682 14663 Z= 0.267 Chirality : 0.041 0.197 1583 Planarity : 0.004 0.043 1906 Dihedral : 4.134 17.863 1425 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.95 % Allowed : 12.41 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.22), residues: 1304 helix: 1.31 (0.21), residues: 584 sheet: 0.14 (0.40), residues: 140 loop : 0.18 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 176 HIS 0.016 0.001 HIS B 596 PHE 0.011 0.001 PHE A 386 TYR 0.016 0.002 TYR B 460 ARG 0.008 0.000 ARG A 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4601.78 seconds wall clock time: 82 minutes 15.52 seconds (4935.52 seconds total)