Starting phenix.real_space_refine on Sun Mar 10 21:23:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/03_2024/7s8u_24922.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/03_2024/7s8u_24922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/03_2024/7s8u_24922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/03_2024/7s8u_24922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/03_2024/7s8u_24922.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/03_2024/7s8u_24922.pdb" } resolution = 3.7 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= -0.004 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 3390 2.51 5 N 854 2.21 5 O 931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 677": "OE1" <-> "OE2" 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: 5210 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5210 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 30, 'TRANS': 636} Time building chain proxies: 3.43, per 1000 atoms: 0.66 Number of scatterers: 5210 At special positions: 0 Unit cell: (99.146, 100.26, 99.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 931 8.00 N 854 7.00 C 3390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 565 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 948.2 milliseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 55.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 15 through 45 Processing helix chain 'A' and resid 49 through 78 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 80 through 104 Processing helix chain 'A' and resid 120 through 153 Proline residue: A 142 - end of helix removed outlier: 5.023A pdb=" N SER A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 187 removed outlier: 3.535A pdb=" N SER A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 3.622A pdb=" N VAL A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 217 removed outlier: 4.033A pdb=" N ALA A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.643A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 249 removed outlier: 4.391A pdb=" N CYS A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 272 through 289 Processing helix chain 'A' and resid 291 through 311 removed outlier: 3.948A pdb=" N THR A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Proline residue: A 339 - end of helix removed outlier: 3.857A pdb=" N ASP A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 384 removed outlier: 3.556A pdb=" N ASP A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 609 Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 614 through 638 Processing helix chain 'A' and resid 644 through 669 removed outlier: 4.047A pdb=" N GLU A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 432 removed outlier: 8.225A pdb=" N HIS A 460 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN A 397 " --> pdb=" O HIS A 460 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE A 462 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS A 399 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL A 464 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 401 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA A 466 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A 465 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 419 Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 3.904A pdb=" N GLN A 519 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 488 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 486 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 554 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 574 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 555 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY A 572 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 557 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 570 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 510 removed outlier: 3.667A pdb=" N ASN A 509 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N PHE A 498 " --> pdb=" O ASN A 509 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 823 1.31 - 1.44: 1465 1.44 - 1.56: 2991 1.56 - 1.69: 0 1.69 - 1.82: 59 Bond restraints: 5338 Sorted by residual: bond pdb=" C TRP A 295 " pdb=" O TRP A 295 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.17e-02 7.31e+03 3.04e+01 bond pdb=" C LEU A 176 " pdb=" O LEU A 176 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.15e-02 7.56e+03 2.73e+01 bond pdb=" C VAL A 596 " pdb=" O VAL A 596 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.19e-02 7.06e+03 2.31e+01 bond pdb=" C GLY A 302 " pdb=" O GLY A 302 " ideal model delta sigma weight residual 1.235 1.297 -0.062 1.35e-02 5.49e+03 2.10e+01 bond pdb=" C PHE A 298 " pdb=" O PHE A 298 " ideal model delta sigma weight residual 1.236 1.288 -0.052 1.15e-02 7.56e+03 2.01e+01 ... (remaining 5333 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.28: 171 106.28 - 113.30: 2802 113.30 - 120.32: 2156 120.32 - 127.34: 2072 127.34 - 134.36: 50 Bond angle restraints: 7251 Sorted by residual: angle pdb=" CA PRO A 183 " pdb=" N PRO A 183 " pdb=" CD PRO A 183 " ideal model delta sigma weight residual 112.00 99.95 12.05 1.40e+00 5.10e-01 7.40e+01 angle pdb=" C PHE A 294 " pdb=" N TRP A 295 " pdb=" CA TRP A 295 " ideal model delta sigma weight residual 120.28 111.61 8.67 1.34e+00 5.57e-01 4.19e+01 angle pdb=" N GLN A 300 " pdb=" CA GLN A 300 " pdb=" C GLN A 300 " ideal model delta sigma weight residual 111.28 104.30 6.98 1.09e+00 8.42e-01 4.10e+01 angle pdb=" C LEU A 38 " pdb=" N ILE A 39 " pdb=" CA ILE A 39 " ideal model delta sigma weight residual 120.56 113.27 7.29 1.26e+00 6.30e-01 3.35e+01 angle pdb=" N GLN A 327 " pdb=" CA GLN A 327 " pdb=" C GLN A 327 " ideal model delta sigma weight residual 112.54 105.50 7.04 1.22e+00 6.72e-01 3.33e+01 ... (remaining 7246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 2834 16.07 - 32.14: 223 32.14 - 48.21: 57 48.21 - 64.28: 21 64.28 - 80.35: 8 Dihedral angle restraints: 3143 sinusoidal: 1218 harmonic: 1925 Sorted by residual: dihedral pdb=" C ILE A 585 " pdb=" N ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta harmonic sigma weight residual -122.00 -135.18 13.18 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta harmonic sigma weight residual 123.40 135.00 -11.60 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" C ILE A 289 " pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" CB ILE A 289 " ideal model delta harmonic sigma weight residual -122.00 -131.07 9.07 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 3140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 573 0.060 - 0.120: 180 0.120 - 0.181: 54 0.181 - 0.241: 18 0.241 - 0.301: 2 Chirality restraints: 827 Sorted by residual: chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE A 585 " pdb=" CA ILE A 585 " pdb=" CG1 ILE A 585 " pdb=" CG2 ILE A 585 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 824 not shown) Planarity restraints: 917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 182 " -0.082 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO A 183 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 302 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLY A 302 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY A 302 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 303 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 39 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ILE A 39 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 39 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 40 " 0.014 2.00e-02 2.50e+03 ... (remaining 914 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 983 2.77 - 3.31: 5547 3.31 - 3.84: 8613 3.84 - 4.37: 9757 4.37 - 4.90: 16386 Nonbonded interactions: 41286 Sorted by model distance: nonbonded pdb=" OG1 THR A 555 " pdb=" O PHE A 571 " model vdw 2.243 2.440 nonbonded pdb=" O VAL A 123 " pdb=" OG SER A 126 " model vdw 2.325 2.440 nonbonded pdb=" O GLN A 301 " pdb=" C GLY A 302 " model vdw 2.354 3.270 nonbonded pdb=" OG SER A 536 " pdb=" OE1 GLN A 538 " model vdw 2.367 2.440 nonbonded pdb=" O ILE A 56 " pdb=" OG1 THR A 59 " model vdw 2.382 2.440 ... (remaining 41281 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 group one per residue 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: 0.410 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: 1.970 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 18.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 5338 Z= 0.505 Angle : 1.188 12.046 7251 Z= 0.848 Chirality : 0.070 0.301 827 Planarity : 0.007 0.117 917 Dihedral : 14.003 80.348 1904 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 1.20 % Allowed : 8.27 % Favored : 90.53 % Rotamer: Outliers : 4.56 % Allowed : 3.68 % Favored : 91.75 % Cbeta Deviations : 0.16 % 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: -1.14 (0.33), residues: 665 helix: 0.16 (0.28), residues: 339 sheet: 1.49 (0.72), residues: 54 loop : -2.48 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 622 HIS 0.004 0.001 HIS A 193 PHE 0.015 0.002 PHE A 356 TYR 0.025 0.002 TYR A 41 ARG 0.004 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 0.595 Fit side-chains REVERT: A 76 ASP cc_start: 0.6653 (t70) cc_final: 0.6325 (m-30) REVERT: A 183 PRO cc_start: 0.8466 (OUTLIER) cc_final: 0.7871 (Cg_endo) REVERT: A 286 PHE cc_start: 0.7024 (m-10) cc_final: 0.6651 (t80) REVERT: A 458 HIS cc_start: 0.4926 (m90) cc_final: 0.4489 (m90) REVERT: A 465 TRP cc_start: 0.3603 (p90) cc_final: 0.2983 (p90) REVERT: A 502 MET cc_start: 0.6655 (tmm) cc_final: 0.6420 (ppp) REVERT: A 541 ARG cc_start: 0.6430 (ptt180) cc_final: 0.6163 (ptt180) REVERT: A 632 ILE cc_start: 0.8696 (mt) cc_final: 0.8402 (mt) outliers start: 26 outliers final: 7 residues processed: 211 average time/residue: 0.1664 time to fit residues: 45.3050 Evaluate side-chains 156 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 183 PRO Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 PRO Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 586 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 315 GLN A 519 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5338 Z= 0.216 Angle : 0.723 8.115 7251 Z= 0.383 Chirality : 0.047 0.228 827 Planarity : 0.006 0.065 917 Dihedral : 6.500 50.058 729 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.82 % Favored : 91.73 % Rotamer: Outliers : 4.91 % Allowed : 13.86 % Favored : 81.23 % 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: -0.66 (0.32), residues: 665 helix: 0.79 (0.27), residues: 353 sheet: 1.68 (0.66), residues: 52 loop : -2.74 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 622 HIS 0.007 0.001 HIS A 58 PHE 0.034 0.002 PHE A 243 TYR 0.021 0.002 TYR A 588 ARG 0.004 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 0.551 Fit side-chains REVERT: A 24 GLU cc_start: 0.7784 (tp30) cc_final: 0.7578 (tp30) REVERT: A 76 ASP cc_start: 0.6583 (t70) cc_final: 0.6278 (m-30) REVERT: A 285 MET cc_start: 0.7485 (ttp) cc_final: 0.6996 (mtp) REVERT: A 286 PHE cc_start: 0.6794 (m-10) cc_final: 0.6126 (t80) REVERT: A 326 MET cc_start: 0.8063 (mmm) cc_final: 0.7747 (mmm) REVERT: A 327 GLN cc_start: 0.8888 (mp10) cc_final: 0.8512 (mp10) REVERT: A 595 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 632 ILE cc_start: 0.8776 (mt) cc_final: 0.8468 (mt) REVERT: A 644 LYS cc_start: 0.7201 (pttm) cc_final: 0.6640 (pttm) REVERT: A 648 GLU cc_start: 0.7542 (pm20) cc_final: 0.7232 (pm20) outliers start: 28 outliers final: 15 residues processed: 162 average time/residue: 0.1597 time to fit residues: 33.9458 Evaluate side-chains 146 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 585 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.0040 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5338 Z= 0.215 Angle : 0.708 9.616 7251 Z= 0.364 Chirality : 0.044 0.210 827 Planarity : 0.005 0.069 917 Dihedral : 6.239 58.426 719 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.57 % Favored : 91.13 % Rotamer: Outliers : 4.39 % Allowed : 18.42 % Favored : 77.19 % 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: -0.37 (0.32), residues: 665 helix: 0.94 (0.27), residues: 354 sheet: 1.65 (0.59), residues: 62 loop : -2.63 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.027 0.002 PHE A 243 TYR 0.019 0.002 TYR A 224 ARG 0.003 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 0.552 Fit side-chains REVERT: A 24 GLU cc_start: 0.7631 (tp30) cc_final: 0.7417 (mm-30) REVERT: A 76 ASP cc_start: 0.6682 (t70) cc_final: 0.6341 (m-30) REVERT: A 225 LYS cc_start: 0.7889 (tppt) cc_final: 0.7669 (tppt) REVERT: A 285 MET cc_start: 0.7453 (ttp) cc_final: 0.7003 (mtp) REVERT: A 286 PHE cc_start: 0.6809 (m-10) cc_final: 0.6110 (t80) REVERT: A 301 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.4348 (tm130) REVERT: A 326 MET cc_start: 0.7961 (mmm) cc_final: 0.7610 (mmm) REVERT: A 502 MET cc_start: 0.5643 (tmm) cc_final: 0.5442 (tmm) REVERT: A 595 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 632 ILE cc_start: 0.8777 (mt) cc_final: 0.8461 (mt) REVERT: A 644 LYS cc_start: 0.7223 (pttm) cc_final: 0.6720 (pttm) outliers start: 25 outliers final: 20 residues processed: 145 average time/residue: 0.1473 time to fit residues: 28.2903 Evaluate side-chains 150 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5338 Z= 0.204 Angle : 0.683 8.535 7251 Z= 0.353 Chirality : 0.044 0.167 827 Planarity : 0.005 0.067 917 Dihedral : 6.037 50.025 719 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.87 % Favored : 90.83 % Rotamer: Outliers : 5.09 % Allowed : 20.18 % Favored : 74.74 % 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: -0.23 (0.33), residues: 665 helix: 1.04 (0.27), residues: 356 sheet: 1.38 (0.58), residues: 64 loop : -2.49 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.020 0.002 PHE A 243 TYR 0.019 0.001 TYR A 224 ARG 0.005 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.620 Fit side-chains REVERT: A 76 ASP cc_start: 0.6725 (t70) cc_final: 0.6375 (m-30) REVERT: A 285 MET cc_start: 0.7521 (ttp) cc_final: 0.7121 (mtp) REVERT: A 286 PHE cc_start: 0.6783 (m-10) cc_final: 0.6119 (t80) REVERT: A 301 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.4579 (tm130) REVERT: A 326 MET cc_start: 0.7860 (mmm) cc_final: 0.7506 (mmm) REVERT: A 371 MET cc_start: 0.7249 (mmm) cc_final: 0.6874 (mtt) REVERT: A 558 MET cc_start: 0.5665 (mmp) cc_final: 0.5202 (mmp) REVERT: A 595 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 632 ILE cc_start: 0.8817 (mt) cc_final: 0.8515 (mt) REVERT: A 644 LYS cc_start: 0.7324 (pttm) cc_final: 0.6619 (pttm) REVERT: A 648 GLU cc_start: 0.7345 (mp0) cc_final: 0.7121 (pm20) outliers start: 29 outliers final: 22 residues processed: 146 average time/residue: 0.1492 time to fit residues: 29.4836 Evaluate side-chains 154 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5338 Z= 0.254 Angle : 0.727 8.595 7251 Z= 0.382 Chirality : 0.046 0.188 827 Planarity : 0.005 0.063 917 Dihedral : 5.987 48.549 717 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.32 % Favored : 90.23 % Rotamer: Outliers : 6.14 % Allowed : 20.35 % Favored : 73.51 % 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: -0.32 (0.33), residues: 665 helix: 0.99 (0.27), residues: 357 sheet: 1.24 (0.58), residues: 64 loop : -2.55 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 646 HIS 0.016 0.002 HIS A 193 PHE 0.021 0.002 PHE A 356 TYR 0.016 0.002 TYR A 41 ARG 0.006 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 76 ASP cc_start: 0.6542 (t70) cc_final: 0.6303 (m-30) REVERT: A 285 MET cc_start: 0.7709 (ttp) cc_final: 0.7295 (mtp) REVERT: A 286 PHE cc_start: 0.7015 (m-10) cc_final: 0.6254 (t80) REVERT: A 321 ILE cc_start: 0.8776 (tp) cc_final: 0.8569 (tp) REVERT: A 356 PHE cc_start: 0.7566 (t80) cc_final: 0.7291 (t80) REVERT: A 556 TYR cc_start: 0.7130 (m-10) cc_final: 0.6754 (m-10) REVERT: A 558 MET cc_start: 0.6074 (mmp) cc_final: 0.5546 (mmp) REVERT: A 595 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 632 ILE cc_start: 0.8886 (mt) cc_final: 0.8594 (mt) REVERT: A 644 LYS cc_start: 0.7475 (pttm) cc_final: 0.7051 (pttm) REVERT: A 657 LEU cc_start: 0.7244 (tp) cc_final: 0.7009 (mt) outliers start: 35 outliers final: 27 residues processed: 154 average time/residue: 0.1363 time to fit residues: 28.5291 Evaluate side-chains 156 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5338 Z= 0.193 Angle : 0.682 8.181 7251 Z= 0.352 Chirality : 0.044 0.162 827 Planarity : 0.005 0.061 917 Dihedral : 5.759 42.614 717 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.72 % Favored : 90.83 % Rotamer: Outliers : 5.61 % Allowed : 22.46 % Favored : 71.93 % 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 (0.33), residues: 665 helix: 1.14 (0.27), residues: 357 sheet: 1.06 (0.60), residues: 66 loop : -2.66 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.018 0.001 PHE A 356 TYR 0.020 0.002 TYR A 224 ARG 0.002 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 0.780 Fit side-chains REVERT: A 18 PHE cc_start: 0.4261 (OUTLIER) cc_final: 0.3728 (m-80) REVERT: A 76 ASP cc_start: 0.6514 (t70) cc_final: 0.6285 (m-30) REVERT: A 225 LYS cc_start: 0.7607 (tppt) cc_final: 0.7252 (ptmt) REVERT: A 246 THR cc_start: 0.4523 (p) cc_final: 0.4166 (m) REVERT: A 285 MET cc_start: 0.7577 (ttp) cc_final: 0.7172 (mtp) REVERT: A 286 PHE cc_start: 0.6966 (m-10) cc_final: 0.6319 (t80) REVERT: A 301 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.4734 (tm130) REVERT: A 337 MET cc_start: 0.7720 (ttp) cc_final: 0.7339 (ttm) REVERT: A 357 THR cc_start: 0.6236 (OUTLIER) cc_final: 0.5856 (p) REVERT: A 408 MET cc_start: 0.6466 (mpp) cc_final: 0.5973 (mpp) REVERT: A 558 MET cc_start: 0.5957 (mmp) cc_final: 0.5534 (mmp) REVERT: A 632 ILE cc_start: 0.8789 (mt) cc_final: 0.8474 (mt) REVERT: A 644 LYS cc_start: 0.7444 (pttm) cc_final: 0.7114 (pttm) REVERT: A 657 LEU cc_start: 0.7257 (tp) cc_final: 0.6972 (mt) outliers start: 32 outliers final: 24 residues processed: 157 average time/residue: 0.1774 time to fit residues: 38.0991 Evaluate side-chains 158 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 0.0870 chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5338 Z= 0.191 Angle : 0.687 8.143 7251 Z= 0.353 Chirality : 0.044 0.201 827 Planarity : 0.005 0.060 917 Dihedral : 5.599 40.352 717 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.57 % Favored : 90.98 % Rotamer: Outliers : 5.44 % Allowed : 24.21 % Favored : 70.35 % 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: -0.31 (0.32), residues: 665 helix: 1.15 (0.27), residues: 356 sheet: 1.07 (0.59), residues: 66 loop : -2.77 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 622 HIS 0.008 0.001 HIS A 193 PHE 0.031 0.001 PHE A 298 TYR 0.017 0.001 TYR A 41 ARG 0.002 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 0.516 Fit side-chains REVERT: A 18 PHE cc_start: 0.4351 (OUTLIER) cc_final: 0.3911 (m-80) REVERT: A 76 ASP cc_start: 0.6529 (t70) cc_final: 0.6288 (m-30) REVERT: A 246 THR cc_start: 0.4526 (p) cc_final: 0.4154 (m) REVERT: A 273 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6130 (mmp80) REVERT: A 285 MET cc_start: 0.7451 (ttp) cc_final: 0.7073 (mtp) REVERT: A 286 PHE cc_start: 0.6945 (m-10) cc_final: 0.6313 (t80) REVERT: A 301 GLN cc_start: 0.5822 (OUTLIER) cc_final: 0.4266 (tm130) REVERT: A 337 MET cc_start: 0.7719 (ttp) cc_final: 0.7347 (ttm) REVERT: A 357 THR cc_start: 0.6321 (OUTLIER) cc_final: 0.5668 (p) REVERT: A 408 MET cc_start: 0.6260 (mpp) cc_final: 0.5771 (mpp) REVERT: A 417 MET cc_start: 0.4042 (mmm) cc_final: 0.3778 (ptm) REVERT: A 558 MET cc_start: 0.5972 (mmp) cc_final: 0.5574 (mmp) REVERT: A 568 LEU cc_start: 0.8167 (tp) cc_final: 0.7960 (tp) REVERT: A 632 ILE cc_start: 0.8753 (mt) cc_final: 0.8432 (mt) REVERT: A 642 PHE cc_start: 0.4869 (OUTLIER) cc_final: 0.4583 (t80) REVERT: A 644 LYS cc_start: 0.7493 (pttm) cc_final: 0.7134 (pttm) REVERT: A 657 LEU cc_start: 0.7272 (tp) cc_final: 0.6967 (mt) outliers start: 31 outliers final: 24 residues processed: 156 average time/residue: 0.1335 time to fit residues: 28.2595 Evaluate side-chains 159 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5338 Z= 0.213 Angle : 0.716 9.684 7251 Z= 0.364 Chirality : 0.044 0.177 827 Planarity : 0.005 0.059 917 Dihedral : 5.579 40.455 717 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.87 % Favored : 90.68 % Rotamer: Outliers : 5.79 % Allowed : 24.56 % Favored : 69.65 % 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 (0.32), residues: 665 helix: 1.11 (0.27), residues: 357 sheet: 1.03 (0.58), residues: 66 loop : -2.60 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 622 HIS 0.006 0.001 HIS A 251 PHE 0.028 0.002 PHE A 356 TYR 0.016 0.001 TYR A 41 ARG 0.003 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 0.583 Fit side-chains REVERT: A 18 PHE cc_start: 0.3314 (OUTLIER) cc_final: 0.3015 (m-80) REVERT: A 76 ASP cc_start: 0.6526 (t70) cc_final: 0.6291 (m-30) REVERT: A 246 THR cc_start: 0.4453 (p) cc_final: 0.4087 (m) REVERT: A 273 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6138 (mmp80) REVERT: A 285 MET cc_start: 0.7491 (ttp) cc_final: 0.7108 (mtp) REVERT: A 286 PHE cc_start: 0.6961 (m-10) cc_final: 0.6102 (t80) REVERT: A 301 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.4307 (tm130) REVERT: A 337 MET cc_start: 0.7728 (ttp) cc_final: 0.7345 (ttm) REVERT: A 357 THR cc_start: 0.6317 (OUTLIER) cc_final: 0.5832 (p) REVERT: A 408 MET cc_start: 0.6474 (mpp) cc_final: 0.5917 (mpp) REVERT: A 558 MET cc_start: 0.6079 (mmp) cc_final: 0.5650 (mmp) REVERT: A 632 ILE cc_start: 0.8768 (mt) cc_final: 0.8457 (mt) REVERT: A 644 LYS cc_start: 0.7527 (pttm) cc_final: 0.7169 (pttm) REVERT: A 657 LEU cc_start: 0.7268 (tp) cc_final: 0.6994 (mt) outliers start: 33 outliers final: 27 residues processed: 148 average time/residue: 0.1359 time to fit residues: 27.3316 Evaluate side-chains 159 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.0040 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 62 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5338 Z= 0.196 Angle : 0.707 9.004 7251 Z= 0.359 Chirality : 0.045 0.180 827 Planarity : 0.005 0.060 917 Dihedral : 5.420 40.080 717 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.12 % Favored : 91.43 % Rotamer: Outliers : 5.44 % Allowed : 25.61 % Favored : 68.95 % 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: -0.19 (0.32), residues: 665 helix: 1.12 (0.27), residues: 356 sheet: 1.14 (0.58), residues: 66 loop : -2.51 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 465 HIS 0.006 0.001 HIS A 58 PHE 0.011 0.001 PHE A 356 TYR 0.016 0.001 TYR A 41 ARG 0.001 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 18 PHE cc_start: 0.4386 (OUTLIER) cc_final: 0.4043 (m-80) REVERT: A 76 ASP cc_start: 0.6592 (t70) cc_final: 0.6284 (m-30) REVERT: A 246 THR cc_start: 0.4433 (p) cc_final: 0.4066 (m) REVERT: A 265 TRP cc_start: 0.6230 (t-100) cc_final: 0.5981 (t-100) REVERT: A 273 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6101 (mmp80) REVERT: A 285 MET cc_start: 0.7487 (ttp) cc_final: 0.7139 (mtp) REVERT: A 286 PHE cc_start: 0.6743 (m-10) cc_final: 0.6061 (t80) REVERT: A 337 MET cc_start: 0.7727 (ttp) cc_final: 0.7348 (ttm) REVERT: A 357 THR cc_start: 0.5869 (OUTLIER) cc_final: 0.5347 (p) REVERT: A 390 PHE cc_start: 0.7023 (m-10) cc_final: 0.6616 (m-10) REVERT: A 408 MET cc_start: 0.6428 (mpp) cc_final: 0.5879 (mpp) REVERT: A 417 MET cc_start: 0.4046 (mmm) cc_final: 0.3738 (ptm) REVERT: A 556 TYR cc_start: 0.6983 (m-10) cc_final: 0.6660 (m-10) REVERT: A 558 MET cc_start: 0.6015 (mmp) cc_final: 0.5642 (mmp) REVERT: A 632 ILE cc_start: 0.8727 (mt) cc_final: 0.8402 (mt) REVERT: A 642 PHE cc_start: 0.4763 (OUTLIER) cc_final: 0.4410 (t80) REVERT: A 644 LYS cc_start: 0.7478 (pttm) cc_final: 0.6584 (pttm) REVERT: A 648 GLU cc_start: 0.7129 (mp0) cc_final: 0.6842 (pm20) REVERT: A 657 LEU cc_start: 0.7274 (tp) cc_final: 0.6968 (mt) outliers start: 31 outliers final: 24 residues processed: 149 average time/residue: 0.1427 time to fit residues: 29.0012 Evaluate side-chains 156 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 642 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 14 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5338 Z= 0.206 Angle : 0.711 8.736 7251 Z= 0.363 Chirality : 0.044 0.173 827 Planarity : 0.005 0.059 917 Dihedral : 5.476 40.094 717 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.72 % Favored : 90.83 % Rotamer: Outliers : 5.44 % Allowed : 25.79 % Favored : 68.77 % 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: -0.24 (0.32), residues: 665 helix: 1.15 (0.27), residues: 356 sheet: 1.22 (0.59), residues: 66 loop : -2.67 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.005 0.001 HIS A 58 PHE 0.015 0.001 PHE A 298 TYR 0.015 0.001 TYR A 41 ARG 0.002 0.000 ARG A 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 18 PHE cc_start: 0.4278 (OUTLIER) cc_final: 0.4022 (m-80) REVERT: A 76 ASP cc_start: 0.6594 (t70) cc_final: 0.6259 (m-30) REVERT: A 246 THR cc_start: 0.4437 (p) cc_final: 0.4053 (m) REVERT: A 265 TRP cc_start: 0.6317 (t-100) cc_final: 0.6093 (t-100) REVERT: A 273 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6073 (mmp80) REVERT: A 285 MET cc_start: 0.7281 (ttp) cc_final: 0.7008 (mtp) REVERT: A 286 PHE cc_start: 0.6742 (m-10) cc_final: 0.6136 (t80) REVERT: A 311 THR cc_start: 0.7774 (p) cc_final: 0.7400 (t) REVERT: A 324 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8027 (p0) REVERT: A 337 MET cc_start: 0.7736 (ttp) cc_final: 0.7364 (ttm) REVERT: A 357 THR cc_start: 0.5880 (OUTLIER) cc_final: 0.5337 (p) REVERT: A 408 MET cc_start: 0.6468 (mpp) cc_final: 0.5914 (mpp) REVERT: A 417 MET cc_start: 0.4086 (mmm) cc_final: 0.3737 (ptm) REVERT: A 556 TYR cc_start: 0.7066 (m-10) cc_final: 0.6769 (m-10) REVERT: A 558 MET cc_start: 0.6081 (mmp) cc_final: 0.5657 (mmp) REVERT: A 560 ARG cc_start: 0.6404 (mtt90) cc_final: 0.5900 (ptm160) REVERT: A 632 ILE cc_start: 0.8751 (mt) cc_final: 0.8430 (mt) REVERT: A 642 PHE cc_start: 0.4768 (OUTLIER) cc_final: 0.4413 (t80) REVERT: A 644 LYS cc_start: 0.7507 (pttm) cc_final: 0.6557 (pttm) REVERT: A 648 GLU cc_start: 0.7127 (mp0) cc_final: 0.6868 (pm20) REVERT: A 657 LEU cc_start: 0.7285 (tp) cc_final: 0.6986 (mt) outliers start: 31 outliers final: 24 residues processed: 144 average time/residue: 0.1475 time to fit residues: 28.4082 Evaluate side-chains 156 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 642 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 53 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** 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 = 0.4613 r_free = 0.4613 target = 0.223583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.202200 restraints weight = 11359.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.206661 restraints weight = 7227.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.207578 restraints weight = 4332.192| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5338 Z= 0.203 Angle : 0.706 8.773 7251 Z= 0.360 Chirality : 0.045 0.177 827 Planarity : 0.005 0.056 917 Dihedral : 5.404 40.159 717 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.87 % Favored : 90.68 % Rotamer: Outliers : 5.61 % Allowed : 25.79 % Favored : 68.60 % 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: -0.14 (0.33), residues: 665 helix: 1.20 (0.27), residues: 354 sheet: 1.14 (0.58), residues: 66 loop : -2.51 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 465 HIS 0.010 0.001 HIS A 193 PHE 0.013 0.001 PHE A 18 TYR 0.015 0.001 TYR A 41 ARG 0.002 0.000 ARG A 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1539.24 seconds wall clock time: 28 minutes 37.20 seconds (1717.20 seconds total)