Starting phenix.real_space_refine on Mon Mar 11 16:11:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/03_2024/8jek_36191_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/03_2024/8jek_36191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/03_2024/8jek_36191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/03_2024/8jek_36191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/03_2024/8jek_36191_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/03_2024/8jek_36191_updated.pdb" } resolution = 2.7 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= 0.002 sd= 0.047 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5440 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ASP 433": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8623 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4167 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 186 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1} Unresolved non-hydrogen planarities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 51.827 64.206 39.994 1.00 27.34 S ATOM 1738 SG CYS A 222 50.728 68.892 44.226 1.00 28.24 S ATOM 1698 SG CYS A 216 52.433 63.595 46.715 1.00 34.01 S Time building chain proxies: 5.13, per 1000 atoms: 0.59 Number of scatterers: 8623 At special positions: 0 Unit cell: (104.4, 108.75, 77.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1639 8.00 N 1490 7.00 C 5440 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 34.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 139 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 356 through 359 removed outlier: 3.588A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 388 through 401 removed outlier: 3.544A pdb=" N ASP A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 461 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 523 through 540 Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 128 through 140 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 186 through 196 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.972A pdb=" N HIS C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 266 through 273 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 280 through 292 removed outlier: 3.718A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.752A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'C' and resid 409 through 422 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 446 through 450 Processing sheet with id= A, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.193A pdb=" N LYS A 247 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.691A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 326 through 332 removed outlier: 4.811A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 70 through 73 Processing sheet with id= G, first strand: chain 'C' and resid 223 through 225 Processing sheet with id= H, first strand: chain 'C' and resid 384 through 388 256 hydrogen bonds defined for protein. 708 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: 2.36 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8764 1.76 - 2.31: 90 2.31 - 2.85: 0 2.85 - 3.39: 0 3.39 - 3.94: 3 Bond restraints: 8857 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.935 -1.635 2.00e-02 2.50e+03 6.69e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.818 -1.585 2.00e-02 2.50e+03 6.28e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.789 -1.531 2.00e-02 2.50e+03 5.86e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 8852 not shown) Histogram of bond angle deviations from ideal: 39.22 - 66.37: 4 66.37 - 93.52: 20 93.52 - 120.67: 8739 120.67 - 147.83: 3335 147.83 - 174.98: 6 Bond angle restraints: 12104 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.44 47.31 3.00e+00 1.11e-01 2.49e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 67.16 45.43 3.00e+00 1.11e-01 2.29e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 68.87 34.38 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 69.18 34.08 3.00e+00 1.11e-01 1.29e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 39.22 32.53 3.00e+00 1.11e-01 1.18e+02 ... (remaining 12099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5052 34.62 - 69.24: 170 69.24 - 103.86: 18 103.86 - 138.48: 0 138.48 - 173.09: 1 Dihedral angle restraints: 5241 sinusoidal: 2089 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -119.72 -60.28 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" C37 U10 C 504 " pdb=" C38 U10 C 504 " pdb=" C39 U10 C 504 " pdb=" C41 U10 C 504 " ideal model delta sinusoidal sigma weight residual -5.63 167.47 -173.09 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2C HEC C 502 " pdb=" C3C HEC C 502 " pdb=" CAC HEC C 502 " pdb=" CBC HEC C 502 " ideal model delta sinusoidal sigma weight residual -120.00 -38.15 -81.85 2 1.00e+01 1.00e-02 4.70e+01 ... (remaining 5238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.462: 1276 3.462 - 6.924: 0 6.924 - 10.386: 0 10.386 - 13.848: 0 13.848 - 17.310: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.54 17.31 2.00e-01 2.50e+01 7.49e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3' FAD A 601 " pdb=" C2' FAD A 601 " pdb=" C4' FAD A 601 " pdb=" O3' FAD A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.34 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1274 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " -0.001 2.00e-02 2.50e+03 9.06e-02 1.44e+02 pdb=" C1M U10 C 504 " 0.063 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.028 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " -0.133 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " 0.144 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.015 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.033 2.00e-02 2.50e+03 6.99e-02 4.88e+01 pdb=" CGD HEC C 501 " 0.121 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.043 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " -0.101 5.00e-02 4.00e+02 1.56e-01 3.91e+01 pdb=" N PRO A 81 " 0.271 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.081 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 457 2.72 - 3.27: 8623 3.27 - 3.81: 15313 3.81 - 4.36: 19875 4.36 - 4.90: 32533 Nonbonded interactions: 76801 Sorted by model distance: nonbonded pdb=" O ALA C 397 " pdb=" OG SER C 402 " model vdw 2.178 2.440 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.189 2.440 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.195 2.440 nonbonded pdb=" OG SER C 354 " pdb=" OD1 ASP C 356 " model vdw 2.219 2.440 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.257 2.688 ... (remaining 76796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 5.010 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.280 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.031 1.635 8857 Z= 1.372 Angle : 1.339 47.314 12104 Z= 0.518 Chirality : 0.487 17.310 1277 Planarity : 0.008 0.156 1572 Dihedral : 17.134 173.095 3229 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.69 % Allowed : 13.21 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.19 (0.25), residues: 1083 helix: 1.47 (0.28), residues: 363 sheet: 0.37 (0.64), residues: 72 loop : -0.70 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 111 HIS 0.006 0.001 HIS A 110 PHE 0.017 0.001 PHE A 270 TYR 0.014 0.001 TYR A 79 ARG 0.002 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.943 Fit side-chains REVERT: A 505 ASN cc_start: 0.7804 (t0) cc_final: 0.7253 (t0) REVERT: C 315 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.5098 (p90) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 1.0590 time to fit residues: 133.7890 Evaluate side-chains 118 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 8857 Z= 0.349 Angle : 1.420 80.798 12104 Z= 0.523 Chirality : 0.089 2.688 1277 Planarity : 0.006 0.116 1572 Dihedral : 12.489 151.825 1318 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.37 % Rotamer: Outliers : 3.05 % Allowed : 12.30 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 2.99 % Twisted General : 0.10 % 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: 0.06 (0.25), residues: 1083 helix: 1.33 (0.27), residues: 364 sheet: 0.38 (0.63), residues: 73 loop : -0.77 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 111 HIS 0.005 0.001 HIS A 478 PHE 0.020 0.002 PHE A 270 TYR 0.019 0.002 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.819 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 478 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7242 (p-80) REVERT: C 143 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7002 (pttp) outliers start: 27 outliers final: 11 residues processed: 120 average time/residue: 1.0269 time to fit residues: 133.1738 Evaluate side-chains 117 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8857 Z= 0.232 Angle : 1.093 86.949 12104 Z= 0.416 Chirality : 0.061 1.455 1277 Planarity : 0.005 0.096 1572 Dihedral : 11.725 146.821 1309 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.27 % Allowed : 13.21 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1083 helix: 1.42 (0.27), residues: 371 sheet: 0.46 (0.64), residues: 73 loop : -0.67 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 111 HIS 0.005 0.001 HIS A 76 PHE 0.017 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.001 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.7119 (p-80) REVERT: C 118 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.5894 (tpp) REVERT: C 143 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6957 (pttp) outliers start: 29 outliers final: 18 residues processed: 120 average time/residue: 1.0002 time to fit residues: 130.1776 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.0030 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 8857 Z= 0.200 Angle : 1.036 84.016 12104 Z= 0.394 Chirality : 0.059 1.377 1277 Planarity : 0.005 0.096 1572 Dihedral : 11.344 139.410 1309 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.16 % Allowed : 13.88 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.37 (0.26), residues: 1083 helix: 1.55 (0.27), residues: 372 sheet: 0.62 (0.64), residues: 72 loop : -0.60 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 111 HIS 0.004 0.001 HIS A 110 PHE 0.016 0.001 PHE A 270 TYR 0.016 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: A 478 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7070 (p-80) REVERT: C 143 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6955 (pttp) outliers start: 28 outliers final: 15 residues processed: 127 average time/residue: 1.0849 time to fit residues: 148.4696 Evaluate side-chains 128 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 8857 Z= 0.320 Angle : 1.082 83.022 12104 Z= 0.421 Chirality : 0.063 1.432 1277 Planarity : 0.006 0.105 1572 Dihedral : 11.578 137.061 1308 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 3.84 % Allowed : 13.43 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.15 (0.26), residues: 1083 helix: 1.31 (0.27), residues: 371 sheet: 0.53 (0.63), residues: 73 loop : -0.69 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 128 HIS 0.006 0.001 HIS C 200 PHE 0.021 0.002 PHE A 270 TYR 0.023 0.002 TYR A 79 ARG 0.006 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7303 (p-80) REVERT: B 183 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5957 (p90) REVERT: C 143 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6972 (pttp) REVERT: C 444 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7621 (tt0) outliers start: 34 outliers final: 20 residues processed: 123 average time/residue: 1.0290 time to fit residues: 137.0023 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 444 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 8857 Z= 0.300 Angle : 1.069 82.242 12104 Z= 0.416 Chirality : 0.063 1.466 1277 Planarity : 0.006 0.106 1572 Dihedral : 11.509 132.391 1308 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 3.39 % Allowed : 14.00 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 2.99 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1083 helix: 1.28 (0.27), residues: 371 sheet: 0.51 (0.64), residues: 73 loop : -0.69 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 173 HIS 0.005 0.001 HIS C 200 PHE 0.020 0.002 PHE A 270 TYR 0.020 0.002 TYR A 79 ARG 0.003 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: A 478 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7278 (p-80) REVERT: C 118 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.5985 (tpt) REVERT: C 143 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6990 (pttp) outliers start: 30 outliers final: 20 residues processed: 119 average time/residue: 0.9981 time to fit residues: 128.7814 Evaluate side-chains 124 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 8857 Z= 0.380 Angle : 1.102 81.465 12104 Z= 0.436 Chirality : 0.066 1.493 1277 Planarity : 0.006 0.112 1572 Dihedral : 11.717 128.519 1308 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 3.72 % Allowed : 13.32 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 2.99 % 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: -0.02 (0.25), residues: 1083 helix: 1.09 (0.27), residues: 371 sheet: 0.49 (0.64), residues: 73 loop : -0.74 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 497 HIS 0.006 0.001 HIS C 200 PHE 0.023 0.002 PHE A 270 TYR 0.021 0.002 TYR A 79 ARG 0.003 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.6957 (tp30) REVERT: A 189 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: A 478 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7388 (p-80) REVERT: A 505 ASN cc_start: 0.7982 (t0) cc_final: 0.7740 (t0) REVERT: A 539 ASN cc_start: 0.8306 (t0) cc_final: 0.7931 (t0) REVERT: B 126 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7064 (mtp180) REVERT: C 118 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.6137 (tpt) REVERT: C 143 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7008 (pttp) REVERT: C 444 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7609 (tt0) outliers start: 33 outliers final: 21 residues processed: 121 average time/residue: 1.0237 time to fit residues: 133.8605 Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 444 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 8857 Z= 0.220 Angle : 1.042 81.851 12104 Z= 0.401 Chirality : 0.062 1.493 1277 Planarity : 0.005 0.108 1572 Dihedral : 11.186 119.110 1308 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 3.05 % Allowed : 14.56 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1083 helix: 1.31 (0.27), residues: 377 sheet: 0.48 (0.64), residues: 73 loop : -0.62 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.005 0.001 HIS A 110 PHE 0.017 0.001 PHE A 270 TYR 0.015 0.001 TYR A 79 ARG 0.003 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: A 478 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7141 (p-80) REVERT: B 126 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6829 (mtp180) REVERT: C 118 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.6008 (tpt) REVERT: C 143 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6949 (pttp) REVERT: C 315 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.5305 (p90) REVERT: C 444 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7599 (tt0) outliers start: 27 outliers final: 16 residues processed: 118 average time/residue: 0.9922 time to fit residues: 126.6807 Evaluate side-chains 127 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 444 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 8857 Z= 0.206 Angle : 1.040 82.189 12104 Z= 0.397 Chirality : 0.061 1.481 1277 Planarity : 0.005 0.110 1572 Dihedral : 10.896 110.626 1308 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.16 % Allowed : 14.22 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.35 (0.26), residues: 1083 helix: 1.44 (0.27), residues: 379 sheet: 0.55 (0.65), residues: 72 loop : -0.55 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.004 0.001 HIS A 110 PHE 0.017 0.001 PHE A 270 TYR 0.014 0.001 TYR A 79 ARG 0.003 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: A 478 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7034 (p-80) REVERT: B 126 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6767 (mtp85) REVERT: C 118 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.5931 (tpt) REVERT: C 143 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6943 (pttp) REVERT: C 315 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.5518 (p90) outliers start: 28 outliers final: 17 residues processed: 122 average time/residue: 0.9982 time to fit residues: 131.8301 Evaluate side-chains 128 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 107 optimal weight: 0.2980 chunk 99 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 8857 Z= 0.238 Angle : 1.055 82.146 12104 Z= 0.405 Chirality : 0.062 1.482 1277 Planarity : 0.005 0.114 1572 Dihedral : 10.952 108.520 1308 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.16 % Allowed : 14.33 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.33 (0.26), residues: 1083 helix: 1.43 (0.27), residues: 378 sheet: 0.56 (0.65), residues: 72 loop : -0.57 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.004 0.001 HIS A 76 PHE 0.018 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.003 0.000 ARG C 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: A 478 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.7128 (p-80) REVERT: B 126 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6796 (mtp180) REVERT: B 183 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.4767 (p90) REVERT: C 118 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.5985 (tpt) REVERT: C 143 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6910 (pttp) outliers start: 28 outliers final: 20 residues processed: 120 average time/residue: 1.0918 time to fit residues: 141.8040 Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.0070 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101170 restraints weight = 9195.852| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.53 r_work: 0.2993 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 8857 Z= 0.255 Angle : 1.064 82.117 12104 Z= 0.410 Chirality : 0.062 1.481 1277 Planarity : 0.006 0.115 1572 Dihedral : 10.998 106.876 1308 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.16 % Allowed : 14.45 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.31 (0.26), residues: 1083 helix: 1.40 (0.27), residues: 378 sheet: 0.53 (0.64), residues: 73 loop : -0.58 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.004 0.001 HIS C 200 PHE 0.019 0.001 PHE A 270 TYR 0.018 0.001 TYR A 79 ARG 0.003 0.000 ARG C 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.85 seconds wall clock time: 55 minutes 50.48 seconds (3350.48 seconds total)