Starting phenix.real_space_refine on Sun Aug 4 21:29:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq6_42462/08_2024/8uq6_42462.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq6_42462/08_2024/8uq6_42462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq6_42462/08_2024/8uq6_42462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq6_42462/08_2024/8uq6_42462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq6_42462/08_2024/8uq6_42462.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq6_42462/08_2024/8uq6_42462.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 3734 2.51 5 N 1073 2.21 5 O 1147 1.98 5 H 5689 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 653": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11700 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 11700 Classifications: {'peptide': 765} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 6, 'PTRANS': 58, 'TRANS': 700} Chain breaks: 1 Time building chain proxies: 6.48, per 1000 atoms: 0.55 Number of scatterers: 11700 At special positions: 0 Unit cell: (80.311, 97.02, 111.034, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1147 8.00 N 1073 7.00 C 3734 6.00 H 5689 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 6.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 67 through 70 removed outlier: 3.787A pdb=" N GLU A 70 " --> pdb=" O HIS A 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.778A pdb=" N LYS A 227 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.648A pdb=" N THR A 303 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 799 through 804 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA4, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.538A pdb=" N THR A 439 " --> pdb=" O TRP A 446 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TRP A 446 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 441 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 496 Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619 Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 703 Processing sheet with id=AA9, first strand: chain 'A' and resid 763 through 766 removed outlier: 5.655A pdb=" N LEU A 764 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 775 " --> pdb=" O LEU A 764 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 90 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 5682 1.13 - 1.30: 1093 1.30 - 1.48: 2438 1.48 - 1.66: 2593 1.66 - 1.84: 67 Bond restraints: 11873 Sorted by residual: bond pdb=" CE3 TRP A 299 " pdb=" HE3 TRP A 299 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER A 292 " pdb=" H SER A 292 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CH2 TRP A 244 " pdb=" HH2 TRP A 244 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE2 PHE A 658 " pdb=" HE2 PHE A 658 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N TYR A 633 " pdb=" H TYR A 633 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 ... (remaining 11868 not shown) Histogram of bond angle deviations from ideal: 72.16 - 84.92: 8 84.92 - 97.69: 9 97.69 - 110.45: 10855 110.45 - 123.22: 9481 123.22 - 135.99: 1073 Bond angle restraints: 21426 Sorted by residual: angle pdb=" C ARG A 386 " pdb=" CA ARG A 386 " pdb=" HA ARG A 386 " ideal model delta sigma weight residual 109.00 72.16 36.84 3.00e+00 1.11e-01 1.51e+02 angle pdb=" N TYR A 385 " pdb=" CA TYR A 385 " pdb=" HA TYR A 385 " ideal model delta sigma weight residual 110.00 73.80 36.20 3.00e+00 1.11e-01 1.46e+02 angle pdb=" N ASN A 450 " pdb=" CA ASN A 450 " pdb=" HA ASN A 450 " ideal model delta sigma weight residual 110.00 74.61 35.39 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C TYR A 385 " pdb=" CA TYR A 385 " pdb=" HA TYR A 385 " ideal model delta sigma weight residual 109.00 75.27 33.73 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C ASN A 450 " pdb=" CA ASN A 450 " pdb=" HA ASN A 450 " ideal model delta sigma weight residual 109.00 77.16 31.84 3.00e+00 1.11e-01 1.13e+02 ... (remaining 21421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 4828 16.45 - 32.89: 580 32.89 - 49.34: 167 49.34 - 65.79: 104 65.79 - 82.23: 15 Dihedral angle restraints: 5694 sinusoidal: 3086 harmonic: 2608 Sorted by residual: dihedral pdb=" C ARG A 386 " pdb=" N ARG A 386 " pdb=" CA ARG A 386 " pdb=" CB ARG A 386 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C TYR A 385 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " pdb=" CB TYR A 385 " ideal model delta harmonic sigma weight residual -122.60 -137.69 15.09 0 2.50e+00 1.60e-01 3.64e+01 dihedral pdb=" CA GLN A 297 " pdb=" C GLN A 297 " pdb=" N HIS A 298 " pdb=" CA HIS A 298 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 641 0.137 - 0.274: 194 0.274 - 0.410: 26 0.410 - 0.547: 3 0.547 - 0.684: 4 Chirality restraints: 868 Sorted by residual: chirality pdb=" CA ARG A 386 " pdb=" N ARG A 386 " pdb=" C ARG A 386 " pdb=" CB ARG A 386 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA TYR A 385 " pdb=" N TYR A 385 " pdb=" C TYR A 385 " pdb=" CB TYR A 385 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ASN A 450 " pdb=" N ASN A 450 " pdb=" C ASN A 450 " pdb=" CB ASN A 450 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 865 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 62 " 0.051 9.50e-02 1.11e+02 1.82e-01 7.40e+02 pdb=" NE ARG A 62 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 62 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 62 " 0.190 2.00e-02 2.50e+03 pdb=" NH2 ARG A 62 " -0.027 2.00e-02 2.50e+03 pdb="HH11 ARG A 62 " 0.103 2.00e-02 2.50e+03 pdb="HH12 ARG A 62 " -0.390 2.00e-02 2.50e+03 pdb="HH21 ARG A 62 " -0.145 2.00e-02 2.50e+03 pdb="HH22 ARG A 62 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 446 " -0.329 2.00e-02 2.50e+03 1.14e-01 5.18e+02 pdb=" CG TRP A 446 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 446 " 0.088 2.00e-02 2.50e+03 pdb=" CD2 TRP A 446 " 0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 446 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP A 446 " 0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP A 446 " 0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 446 " -0.072 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 446 " 0.042 2.00e-02 2.50e+03 pdb=" CH2 TRP A 446 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 TRP A 446 " 0.044 2.00e-02 2.50e+03 pdb=" HE1 TRP A 446 " 0.101 2.00e-02 2.50e+03 pdb=" HE3 TRP A 446 " 0.123 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 446 " -0.148 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 446 " 0.086 2.00e-02 2.50e+03 pdb=" HH2 TRP A 446 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 704 " 0.283 2.00e-02 2.50e+03 1.12e-01 5.04e+02 pdb=" CG TRP A 704 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 704 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 704 " -0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP A 704 " -0.096 2.00e-02 2.50e+03 pdb=" CE2 TRP A 704 " -0.059 2.00e-02 2.50e+03 pdb=" CE3 TRP A 704 " -0.123 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 704 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 704 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP A 704 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 TRP A 704 " 0.079 2.00e-02 2.50e+03 pdb=" HE1 TRP A 704 " -0.124 2.00e-02 2.50e+03 pdb=" HE3 TRP A 704 " -0.172 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 704 " 0.093 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 704 " 0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP A 704 " 0.156 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 861 2.16 - 2.77: 18837 2.77 - 3.38: 31982 3.38 - 3.99: 38674 3.99 - 4.60: 55478 Nonbonded interactions: 145832 Sorted by model distance: nonbonded pdb=" OD2 ASP A 665 " pdb=" HG SER A 779 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLU A 660 " pdb=" HG1 THR A 662 " model vdw 1.584 2.450 nonbonded pdb=" HG1 THR A 495 " pdb=" HA CYS A 555 " model vdw 1.601 2.270 nonbonded pdb=" OD1 ASP A 441 " pdb=" HG SER A 443 " model vdw 1.603 2.450 nonbonded pdb=" OE1 GLU A 78 " pdb=" HG SER A 82 " model vdw 1.608 2.450 ... (remaining 145827 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: 2.350 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: 0.190 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0070 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 : 0.016 0.072 6184 Z= 1.032 Angle : 2.365 17.659 8410 Z= 1.515 Chirality : 0.133 0.684 868 Planarity : 0.020 0.147 1117 Dihedral : 16.350 82.235 2311 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 4.86 % Allowed : 23.52 % Favored : 71.62 % Rotamer: Outliers : 5.96 % Allowed : 8.35 % Favored : 85.69 % Cbeta Deviations : 1.42 % Peptide Plane: Cis-proline : 9.38 % 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: -4.36 (0.27), residues: 761 helix: -4.84 (0.38), residues: 14 sheet: -2.20 (1.15), residues: 24 loop : -3.27 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.208 0.041 TRP A 446 HIS 0.012 0.004 HIS A 336 PHE 0.073 0.014 PHE A 700 TYR 0.176 0.024 TYR A 552 ARG 0.011 0.001 ARG A 731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 77 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: -0.0107 (tmm) cc_final: -0.0529 (tpp) REVERT: A 342 VAL cc_start: -0.2607 (OUTLIER) cc_final: -0.3227 (m) REVERT: A 632 SER cc_start: 0.0514 (OUTLIER) cc_final: 0.0251 (p) REVERT: A 728 VAL cc_start: 0.4233 (t) cc_final: 0.3563 (t) outliers start: 40 outliers final: 15 residues processed: 113 average time/residue: 0.5233 time to fit residues: 72.0887 Evaluate side-chains 62 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 PRO Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 810 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 212 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS A 775 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0007 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6184 Z= 0.344 Angle : 1.007 11.094 8410 Z= 0.532 Chirality : 0.055 0.440 868 Planarity : 0.009 0.108 1117 Dihedral : 11.531 57.407 869 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 1.31 % Allowed : 18.27 % Favored : 80.42 % Rotamer: Outliers : 3.58 % Allowed : 12.82 % Favored : 83.61 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -4.41 (0.26), residues: 761 helix: -4.48 (0.47), residues: 13 sheet: -2.36 (0.90), residues: 33 loop : -3.32 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 127 HIS 0.007 0.002 HIS A 67 PHE 0.020 0.002 PHE A 94 TYR 0.016 0.002 TYR A 793 ARG 0.007 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: -0.0742 (tmm) cc_final: -0.1282 (mmt) REVERT: A 445 ARG cc_start: 0.3552 (mtm-85) cc_final: 0.3196 (mtt180) outliers start: 24 outliers final: 15 residues processed: 71 average time/residue: 0.3557 time to fit residues: 34.2620 Evaluate side-chains 55 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 734 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.0070 chunk 21 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 46 optimal weight: 50.0000 chunk 19 optimal weight: 0.0050 chunk 69 optimal weight: 0.1980 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0051 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6184 Z= 0.218 Angle : 0.802 8.325 8410 Z= 0.417 Chirality : 0.052 0.431 868 Planarity : 0.008 0.103 1117 Dihedral : 9.498 57.499 845 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.79 % Allowed : 19.97 % Favored : 79.24 % Rotamer: Outliers : 2.83 % Allowed : 14.31 % Favored : 82.86 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.96 (0.28), residues: 761 helix: -4.23 (0.58), residues: 14 sheet: -2.07 (0.90), residues: 33 loop : -2.97 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 446 HIS 0.004 0.001 HIS A 748 PHE 0.018 0.002 PHE A 64 TYR 0.018 0.002 TYR A 233 ARG 0.004 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: -0.3191 (OUTLIER) cc_final: -0.3398 (mtm) REVERT: A 201 MET cc_start: -0.0503 (tmm) cc_final: -0.1024 (mmt) REVERT: A 445 ARG cc_start: 0.3285 (mtm-85) cc_final: 0.2944 (mtt180) outliers start: 19 outliers final: 14 residues processed: 61 average time/residue: 0.3877 time to fit residues: 31.4798 Evaluate side-chains 55 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 734 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 73 optimal weight: 40.0000 chunk 36 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 chunk 19 optimal weight: 9.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 409 HIS A 424 ASN ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0262 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6184 Z= 0.317 Angle : 0.887 8.082 8410 Z= 0.468 Chirality : 0.054 0.418 868 Planarity : 0.009 0.099 1117 Dihedral : 8.909 57.221 844 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 21.55 % Favored : 78.06 % Rotamer: Outliers : 3.73 % Allowed : 13.26 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -4.24 (0.27), residues: 761 helix: -4.24 (0.73), residues: 12 sheet: -2.65 (0.64), residues: 53 loop : -3.16 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 542 HIS 0.011 0.002 HIS A 622 PHE 0.019 0.002 PHE A 94 TYR 0.033 0.002 TYR A 219 ARG 0.005 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 40 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: -0.0408 (mmp) cc_final: -0.0906 (mmt) REVERT: A 201 MET cc_start: -0.0354 (tmm) cc_final: -0.1053 (mtt) REVERT: A 232 ASN cc_start: 0.5770 (p0) cc_final: 0.5187 (m110) REVERT: A 444 VAL cc_start: 0.2796 (OUTLIER) cc_final: 0.2583 (p) REVERT: A 552 TYR cc_start: -0.2894 (OUTLIER) cc_final: -0.3137 (p90) REVERT: A 658 PHE cc_start: 0.3407 (OUTLIER) cc_final: 0.3178 (t80) REVERT: A 679 ASP cc_start: 0.5534 (p0) cc_final: 0.4487 (t70) outliers start: 25 outliers final: 16 residues processed: 65 average time/residue: 0.3739 time to fit residues: 32.3717 Evaluate side-chains 57 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 38 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 734 PHE Chi-restraints excluded: chain A residue 760 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 54 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 40.0000 chunk 18 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 157 ASN A 313 ASN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0283 moved from start: 0.8972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6184 Z= 0.248 Angle : 0.779 7.063 8410 Z= 0.403 Chirality : 0.052 0.420 868 Planarity : 0.008 0.091 1117 Dihedral : 8.142 58.743 842 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 18.92 % Favored : 80.68 % Rotamer: Outliers : 2.98 % Allowed : 15.80 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.87 (0.28), residues: 761 helix: -3.98 (0.95), residues: 12 sheet: -1.51 (0.95), residues: 26 loop : -2.93 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 446 HIS 0.010 0.002 HIS A 622 PHE 0.017 0.001 PHE A 94 TYR 0.016 0.001 TYR A 793 ARG 0.002 0.000 ARG A 795 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: -0.0357 (mmp) cc_final: -0.0841 (mmt) REVERT: A 201 MET cc_start: -0.0352 (tmm) cc_final: -0.1186 (tpp) REVERT: A 658 PHE cc_start: 0.3922 (OUTLIER) cc_final: 0.3514 (t80) outliers start: 20 outliers final: 15 residues processed: 57 average time/residue: 0.4473 time to fit residues: 32.7272 Evaluate side-chains 46 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 777 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 313 ASN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0317 moved from start: 0.9541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6184 Z= 0.217 Angle : 0.730 7.631 8410 Z= 0.377 Chirality : 0.051 0.419 868 Planarity : 0.008 0.087 1117 Dihedral : 7.877 58.900 842 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.53 % Allowed : 19.84 % Favored : 79.63 % Rotamer: Outliers : 3.28 % Allowed : 15.65 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.79 (0.28), residues: 761 helix: -3.97 (0.95), residues: 12 sheet: -1.34 (0.99), residues: 26 loop : -2.89 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 446 HIS 0.006 0.001 HIS A 605 PHE 0.014 0.001 PHE A 94 TYR 0.008 0.001 TYR A 793 ARG 0.003 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 30 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: -0.0309 (mmp) cc_final: -0.0768 (mmt) REVERT: A 201 MET cc_start: -0.0246 (tmm) cc_final: -0.1113 (tpp) REVERT: A 658 PHE cc_start: 0.4162 (OUTLIER) cc_final: 0.3917 (t80) outliers start: 22 outliers final: 17 residues processed: 50 average time/residue: 0.4830 time to fit residues: 30.8025 Evaluate side-chains 48 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 30 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 73 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 734 PHE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 777 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 30.0000 chunk 41 optimal weight: 30.0000 chunk 53 optimal weight: 0.4980 chunk 61 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0296 moved from start: 0.9958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6184 Z= 0.186 Angle : 0.689 7.551 8410 Z= 0.350 Chirality : 0.050 0.419 868 Planarity : 0.007 0.083 1117 Dihedral : 7.500 59.189 842 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.39 % Allowed : 17.61 % Favored : 82.00 % Rotamer: Outliers : 2.68 % Allowed : 16.10 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.71 (0.28), residues: 761 helix: -3.81 (0.91), residues: 12 sheet: -1.45 (0.96), residues: 26 loop : -2.81 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 446 HIS 0.005 0.001 HIS A 605 PHE 0.011 0.001 PHE A 94 TYR 0.011 0.001 TYR A 219 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: -0.0398 (mmp) cc_final: -0.1102 (mmt) REVERT: A 201 MET cc_start: -0.0291 (tmm) cc_final: -0.1146 (tpp) outliers start: 18 outliers final: 14 residues processed: 49 average time/residue: 0.4890 time to fit residues: 30.4320 Evaluate side-chains 43 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 777 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 30.0000 chunk 46 optimal weight: 40.0000 chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 41 optimal weight: 30.0000 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 72 GLN A 215 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0570 moved from start: 1.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6184 Z= 0.351 Angle : 0.922 8.130 8410 Z= 0.494 Chirality : 0.056 0.413 868 Planarity : 0.010 0.107 1117 Dihedral : 8.232 45.595 840 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.53 % Allowed : 25.76 % Favored : 73.72 % Rotamer: Outliers : 3.43 % Allowed : 16.10 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.26 (0.27), residues: 761 helix: -3.43 (1.07), residues: 18 sheet: -1.05 (1.15), residues: 26 loop : -3.27 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 334 HIS 0.011 0.003 HIS A 605 PHE 0.021 0.003 PHE A 700 TYR 0.024 0.003 TYR A 283 ARG 0.008 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 37 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.0321 (mmp) cc_final: -0.1306 (mmt) REVERT: A 193 TYR cc_start: -0.1898 (OUTLIER) cc_final: -0.2236 (m-80) REVERT: A 201 MET cc_start: -0.0414 (tmm) cc_final: -0.1356 (tpp) outliers start: 23 outliers final: 19 residues processed: 58 average time/residue: 0.4461 time to fit residues: 33.2521 Evaluate side-chains 50 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 30 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 777 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.0030 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 44 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 322 ASN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0461 moved from start: 1.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6184 Z= 0.191 Angle : 0.723 11.384 8410 Z= 0.365 Chirality : 0.050 0.419 868 Planarity : 0.007 0.076 1117 Dihedral : 7.346 42.315 840 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.66 % Allowed : 18.27 % Favored : 81.08 % Rotamer: Outliers : 2.68 % Allowed : 16.69 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.94 (0.28), residues: 761 helix: -2.99 (1.42), residues: 12 sheet: -1.59 (1.00), residues: 26 loop : -3.01 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 334 HIS 0.008 0.001 HIS A 605 PHE 0.010 0.001 PHE A 94 TYR 0.015 0.001 TYR A 283 ARG 0.004 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: -0.0307 (mmp) cc_final: -0.1634 (mmt) REVERT: A 201 MET cc_start: -0.0450 (tmm) cc_final: -0.1270 (tpp) outliers start: 18 outliers final: 15 residues processed: 49 average time/residue: 0.5001 time to fit residues: 31.0919 Evaluate side-chains 46 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 31 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 46 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** A 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0561 moved from start: 1.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6184 Z= 0.253 Angle : 0.755 8.730 8410 Z= 0.386 Chirality : 0.051 0.411 868 Planarity : 0.008 0.077 1117 Dihedral : 7.275 41.031 840 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.53 % Allowed : 23.92 % Favored : 75.56 % Rotamer: Outliers : 2.38 % Allowed : 16.84 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.05 (0.27), residues: 761 helix: -3.27 (1.19), residues: 18 sheet: -1.34 (1.03), residues: 26 loop : -3.10 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 334 HIS 0.009 0.001 HIS A 605 PHE 0.012 0.001 PHE A 94 TYR 0.020 0.002 TYR A 283 ARG 0.005 0.001 ARG A 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 31 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: -0.0214 (mmp) cc_final: -0.1542 (mmt) REVERT: A 201 MET cc_start: -0.0283 (tmm) cc_final: -0.1162 (tpp) REVERT: A 276 LEU cc_start: 0.7618 (mm) cc_final: 0.7302 (mp) outliers start: 16 outliers final: 13 residues processed: 46 average time/residue: 0.5203 time to fit residues: 30.2947 Evaluate side-chains 43 residues out of total 671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 30 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 254 TRP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 43 optimal weight: 40.0000 chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 313 ASN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.246747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.236611 restraints weight = 126012.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.238853 restraints weight = 79960.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.240431 restraints weight = 54895.473| |-----------------------------------------------------------------------------| r_work (final): 0.5177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1555 moved from start: 1.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6184 Z= 0.197 Angle : 0.700 9.640 8410 Z= 0.352 Chirality : 0.050 0.414 868 Planarity : 0.007 0.076 1117 Dihedral : 6.935 42.914 839 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.66 % Allowed : 19.84 % Favored : 79.50 % Rotamer: Outliers : 2.38 % Allowed : 16.99 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.96 (0.28), residues: 761 helix: -3.97 (0.81), residues: 23 sheet: -1.34 (1.00), residues: 26 loop : -2.98 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 334 HIS 0.008 0.001 HIS A 605 PHE 0.011 0.001 PHE A 94 TYR 0.012 0.001 TYR A 283 ARG 0.004 0.000 ARG A 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2632.70 seconds wall clock time: 46 minutes 39.45 seconds (2799.45 seconds total)