Starting phenix.real_space_refine on Thu Dec 7 22:12:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/12_2023/7s8u_24922.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/12_2023/7s8u_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_24922/12_2023/7s8u_24922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/12_2023/7s8u_24922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/12_2023/7s8u_24922.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/12_2023/7s8u_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-1.21rc1-5172/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: 4.15, per 1000 atoms: 0.80 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: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.55 Time building geometry restraints manager: 2.20 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: 0.420 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: 1.960 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.670 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.970 ------------------------------------------------------------------------------- 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 : 0.567 Fit side-chains outliers start: 26 outliers final: 7 residues processed: 211 average time/residue: 0.1622 time to fit residues: 44.3169 Evaluate side-chains 154 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.0569 time to fit residues: 1.4237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 315 GLN A 519 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5338 Z= 0.255 Angle : 0.763 8.891 7251 Z= 0.408 Chirality : 0.048 0.193 827 Planarity : 0.006 0.065 917 Dihedral : 5.367 22.906 710 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.57 % Favored : 91.13 % Rotamer: Outliers : 4.56 % Allowed : 13.51 % Favored : 81.93 % 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: -0.86 (0.32), residues: 665 helix: 0.64 (0.27), residues: 353 sheet: 1.35 (0.62), residues: 52 loop : -2.80 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 622 HIS 0.008 0.002 HIS A 58 PHE 0.035 0.002 PHE A 243 TYR 0.023 0.002 TYR A 588 ARG 0.009 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 169 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 0.570 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 155 average time/residue: 0.1637 time to fit residues: 33.1092 Evaluate side-chains 142 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0547 time to fit residues: 2.3115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5338 Z= 0.223 Angle : 0.717 9.818 7251 Z= 0.374 Chirality : 0.045 0.183 827 Planarity : 0.005 0.068 917 Dihedral : 5.089 20.911 710 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.87 % Favored : 90.83 % Rotamer: Outliers : 2.28 % Allowed : 18.60 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.32), residues: 665 helix: 0.86 (0.27), residues: 356 sheet: 1.44 (0.58), residues: 62 loop : -2.69 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 622 HIS 0.007 0.001 HIS A 58 PHE 0.026 0.002 PHE A 243 TYR 0.016 0.002 TYR A 41 ARG 0.003 0.001 ARG A 541 *********************** 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 151 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 144 average time/residue: 0.1507 time to fit residues: 28.9691 Evaluate side-chains 129 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0618 time to fit residues: 1.3236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.4100 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= 0.193 Angle : 0.712 10.243 7251 Z= 0.364 Chirality : 0.044 0.141 827 Planarity : 0.005 0.067 917 Dihedral : 4.903 21.506 710 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.72 % Favored : 90.98 % Rotamer: Outliers : 3.16 % Allowed : 20.70 % Favored : 76.14 % 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: -0.35 (0.33), residues: 665 helix: 1.03 (0.27), residues: 354 sheet: 1.13 (0.61), residues: 64 loop : -2.60 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.007 0.001 HIS A 58 PHE 0.018 0.002 PHE A 373 TYR 0.016 0.001 TYR A 41 ARG 0.003 0.000 ARG A 560 *********************** 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 161 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.567 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 0.1456 time to fit residues: 29.4363 Evaluate side-chains 144 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0982 time to fit residues: 2.5092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 0.0000 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 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 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5338 Z= 0.292 Angle : 0.795 9.217 7251 Z= 0.418 Chirality : 0.048 0.178 827 Planarity : 0.006 0.062 917 Dihedral : 5.268 19.888 710 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.77 % Favored : 89.77 % Rotamer: Outliers : 2.63 % Allowed : 22.81 % Favored : 74.56 % 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: -0.59 (0.32), residues: 665 helix: 0.82 (0.27), residues: 357 sheet: 0.58 (0.66), residues: 56 loop : -2.49 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 646 HIS 0.010 0.002 HIS A 251 PHE 0.032 0.002 PHE A 18 TYR 0.018 0.002 TYR A 57 ARG 0.008 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 149 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.561 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 143 average time/residue: 0.1576 time to fit residues: 29.7733 Evaluate side-chains 140 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0573 time to fit residues: 2.0090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.4969 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= 0.217 Angle : 0.751 8.832 7251 Z= 0.386 Chirality : 0.045 0.174 827 Planarity : 0.005 0.061 917 Dihedral : 5.133 20.433 710 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.72 % Favored : 90.83 % Rotamer: Outliers : 2.28 % Allowed : 24.21 % 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: -0.38 (0.33), residues: 665 helix: 1.03 (0.28), residues: 358 sheet: 0.76 (0.59), residues: 64 loop : -2.60 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 622 HIS 0.007 0.001 HIS A 58 PHE 0.022 0.002 PHE A 298 TYR 0.019 0.002 TYR A 41 ARG 0.003 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 153 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.585 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 0.1414 time to fit residues: 27.3227 Evaluate side-chains 134 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0624 time to fit residues: 1.4144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.5260 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= 0.227 Angle : 0.780 9.769 7251 Z= 0.393 Chirality : 0.046 0.157 827 Planarity : 0.005 0.060 917 Dihedral : 5.064 22.218 710 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.32 % Favored : 90.23 % Rotamer: Outliers : 2.28 % Allowed : 24.91 % Favored : 72.81 % 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: -0.41 (0.33), residues: 665 helix: 0.97 (0.27), residues: 357 sheet: 0.54 (0.58), residues: 64 loop : -2.45 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 622 HIS 0.007 0.001 HIS A 251 PHE 0.020 0.002 PHE A 356 TYR 0.016 0.002 TYR A 288 ARG 0.003 0.000 ARG A 250 *********************** 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 146 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.542 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 142 average time/residue: 0.1437 time to fit residues: 27.4955 Evaluate side-chains 138 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0636 time to fit residues: 1.3546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.5564 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= 0.211 Angle : 0.777 9.665 7251 Z= 0.388 Chirality : 0.046 0.165 827 Planarity : 0.005 0.060 917 Dihedral : 5.104 21.459 710 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.27 % Favored : 91.28 % Rotamer: Outliers : 1.23 % Allowed : 25.26 % 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: -0.39 (0.33), residues: 665 helix: 0.99 (0.27), residues: 353 sheet: 0.49 (0.58), residues: 66 loop : -2.41 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.031 0.002 PHE A 356 TYR 0.014 0.002 TYR A 288 ARG 0.003 0.000 ARG A 547 *********************** 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 137 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.585 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 134 average time/residue: 0.1458 time to fit residues: 26.5268 Evaluate side-chains 127 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0619 time to fit residues: 1.4388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 188 GLN ** 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: 0.6093 moved from start: 0.5711 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= 0.222 Angle : 0.779 9.107 7251 Z= 0.393 Chirality : 0.046 0.173 827 Planarity : 0.005 0.060 917 Dihedral : 5.111 21.667 710 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.17 % Favored : 90.38 % Rotamer: Outliers : 1.05 % Allowed : 26.49 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.32), residues: 665 helix: 1.04 (0.28), residues: 351 sheet: 0.46 (0.66), residues: 56 loop : -2.65 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.033 0.001 PHE A 356 TYR 0.012 0.002 TYR A 41 ARG 0.004 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 135 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.537 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 132 average time/residue: 0.1382 time to fit residues: 24.8426 Evaluate side-chains 125 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0611 time to fit residues: 1.2847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.5855 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= 0.224 Angle : 0.796 10.130 7251 Z= 0.401 Chirality : 0.046 0.157 827 Planarity : 0.005 0.060 917 Dihedral : 4.999 22.642 710 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.17 % Favored : 90.38 % Rotamer: Outliers : 0.53 % Allowed : 27.19 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.33), residues: 665 helix: 0.94 (0.27), residues: 352 sheet: 0.57 (0.62), residues: 66 loop : -2.61 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.012 0.001 PHE A 356 TYR 0.015 0.002 TYR A 588 ARG 0.003 0.000 ARG A 250 ********************** 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 127 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.577 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 126 average time/residue: 0.1404 time to fit residues: 24.1944 Evaluate side-chains 124 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0549 time to fit residues: 0.8923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.221556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.200034 restraints weight = 11536.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.204704 restraints weight = 7414.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.206556 restraints weight = 4253.802| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5338 Z= 0.235 Angle : 0.791 9.272 7251 Z= 0.404 Chirality : 0.046 0.156 827 Planarity : 0.005 0.056 917 Dihedral : 5.090 23.760 710 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.62 % Favored : 89.92 % Rotamer: Outliers : 0.53 % Allowed : 27.19 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.33), residues: 665 helix: 0.93 (0.28), residues: 354 sheet: 0.28 (0.69), residues: 56 loop : -2.37 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 295 HIS 0.007 0.001 HIS A 251 PHE 0.017 0.002 PHE A 18 TYR 0.017 0.002 TYR A 470 ARG 0.004 0.000 ARG A 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1506.10 seconds wall clock time: 28 minutes 11.29 seconds (1691.29 seconds total)