Starting phenix.real_space_refine on Fri Jul 19 07:04:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5s_41060/07_2024/8t5s_41060_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5s_41060/07_2024/8t5s_41060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5s_41060/07_2024/8t5s_41060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5s_41060/07_2024/8t5s_41060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5s_41060/07_2024/8t5s_41060_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5s_41060/07_2024/8t5s_41060_neut.cif" } resolution = 2.9 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= 0.019 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 62 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 4017 2.51 5 N 1187 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A ASP 903": "OD1" <-> "OD2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6799 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5510 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 21, 'TRANS': 671} Chain breaks: 3 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 600 Classifications: {'RNA': 30} Modifications used: {'rna3p_pyr': 30} Link IDs: {'rna3p': 29} Chain: "B" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 660 Classifications: {'RNA': 30} Modifications used: {'rna3p_pur': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4622 SG CYS A 891 33.616 20.824 52.033 1.00141.13 S ATOM 4646 SG CYS A 894 33.665 17.107 51.305 1.00141.12 S ATOM 4947 SG CYS A 945 34.617 18.363 54.764 1.00143.31 S ATOM 4992 SG CYS A 950 36.953 18.952 51.820 1.00149.53 S Time building chain proxies: 4.37, per 1000 atoms: 0.64 Number of scatterers: 6799 At special positions: 0 Unit cell: (89.93, 96.278, 105.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 40 16.00 P 62 15.00 Mg 1 11.99 O 1491 8.00 N 1187 7.00 C 4017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 888.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 894 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 945 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 891 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 950 " Number of angles added : 6 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 54.3% alpha, 9.4% beta 30 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.549A pdb=" N VAL A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.711A pdb=" N VAL A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.743A pdb=" N PHE A 424 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 529 through 557 Processing helix chain 'A' and resid 589 through 605 removed outlier: 4.248A pdb=" N GLN A 593 " --> pdb=" O HIS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.902A pdb=" N ARG A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 654 removed outlier: 3.991A pdb=" N ALA A 642 " --> pdb=" O HIS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 658 through 676 removed outlier: 3.846A pdb=" N GLY A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 697 Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 722 through 728 removed outlier: 4.175A pdb=" N LEU A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 764 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.526A pdb=" N GLU A 778 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 820 through 847 removed outlier: 3.614A pdb=" N ARG A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 859 Processing helix chain 'A' and resid 861 through 881 removed outlier: 3.558A pdb=" N ILE A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 4.218A pdb=" N TRP A 919 " --> pdb=" O PRO A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 removed outlier: 3.873A pdb=" N ILE A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 removed outlier: 3.653A pdb=" N THR A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A1014 " --> pdb=" O MET A1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 374 removed outlier: 3.657A pdb=" N GLN A 372 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA A 344 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA A 394 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE A 346 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 347 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 310 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 311 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 519 through 523 removed outlier: 3.747A pdb=" N VAL A 771 " --> pdb=" O GLU A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AA4, first strand: chain 'A' and resid 911 through 913 removed outlier: 4.204A pdb=" N THR A1000 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 943 through 944 removed outlier: 3.736A pdb=" N GLY A 955 " --> pdb=" O ILE A 943 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2040 1.34 - 1.46: 1372 1.46 - 1.58: 3434 1.58 - 1.70: 121 1.70 - 1.81: 60 Bond restraints: 7027 Sorted by residual: bond pdb=" C TRP A 863 " pdb=" N PRO A 864 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.55e+00 bond pdb=" C4 ADP A1103 " pdb=" C5 ADP A1103 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" CA ASN A 884 " pdb=" CB ASN A 884 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.56e-02 4.11e+03 1.18e+00 bond pdb=" CB ASN A 884 " pdb=" CG ASN A 884 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB GLU A 948 " pdb=" CG GLU A 948 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.28e-01 ... (remaining 7022 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.77: 458 106.77 - 114.00: 4180 114.00 - 121.24: 3354 121.24 - 128.47: 1690 128.47 - 135.70: 92 Bond angle restraints: 9774 Sorted by residual: angle pdb=" CB MET A 650 " pdb=" CG MET A 650 " pdb=" SD MET A 650 " ideal model delta sigma weight residual 112.70 121.81 -9.11 3.00e+00 1.11e-01 9.21e+00 angle pdb=" C ARG A 883 " pdb=" N ASN A 884 " pdb=" CA ASN A 884 " ideal model delta sigma weight residual 123.05 127.75 -4.70 1.57e+00 4.06e-01 8.96e+00 angle pdb=" CA ARG A 865 " pdb=" CB ARG A 865 " pdb=" CG ARG A 865 " ideal model delta sigma weight residual 114.10 119.68 -5.58 2.00e+00 2.50e-01 7.78e+00 angle pdb=" CB ARG A 865 " pdb=" CG ARG A 865 " pdb=" CD ARG A 865 " ideal model delta sigma weight residual 111.30 117.55 -6.25 2.30e+00 1.89e-01 7.37e+00 angle pdb=" CB MET A 445 " pdb=" CG MET A 445 " pdb=" SD MET A 445 " ideal model delta sigma weight residual 112.70 120.79 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 9769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 3849 21.41 - 42.82: 360 42.82 - 64.23: 83 64.23 - 85.64: 7 85.64 - 107.05: 4 Dihedral angle restraints: 4303 sinusoidal: 2272 harmonic: 2031 Sorted by residual: dihedral pdb=" O2A ADP A1103 " pdb=" O3A ADP A1103 " pdb=" PA ADP A1103 " pdb=" PB ADP A1103 " ideal model delta sinusoidal sigma weight residual -60.00 -167.05 107.05 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP A1103 " pdb=" O3A ADP A1103 " pdb=" PB ADP A1103 " pdb=" PA ADP A1103 " ideal model delta sinusoidal sigma weight residual -60.00 8.24 -68.24 1 2.00e+01 2.50e-03 1.51e+01 dihedral pdb=" C4' ADP A1103 " pdb=" C5' ADP A1103 " pdb=" O5' ADP A1103 " pdb=" PA ADP A1103 " ideal model delta sinusoidal sigma weight residual 180.00 114.28 65.72 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 4300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 877 0.029 - 0.059: 175 0.059 - 0.088: 76 0.088 - 0.118: 41 0.118 - 0.147: 4 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CA ASN A 884 " pdb=" N ASN A 884 " pdb=" C ASN A 884 " pdb=" CB ASN A 884 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CB THR A 552 " pdb=" CA THR A 552 " pdb=" OG1 THR A 552 " pdb=" CG2 THR A 552 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA TRP A 863 " pdb=" N TRP A 863 " pdb=" C TRP A 863 " pdb=" CB TRP A 863 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1170 not shown) Planarity restraints: 1037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 863 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 864 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 883 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.20e+00 pdb=" C ARG A 883 " -0.019 2.00e-02 2.50e+03 pdb=" O ARG A 883 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN A 884 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 638 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 639 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " -0.014 5.00e-02 4.00e+02 ... (remaining 1034 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 768 2.75 - 3.29: 6519 3.29 - 3.82: 12585 3.82 - 4.36: 13656 4.36 - 4.90: 21943 Nonbonded interactions: 55471 Sorted by model distance: nonbonded pdb=" ND2 ASN A 908 " pdb=" O2' A B 36 " model vdw 2.212 2.520 nonbonded pdb=" N GLU A 948 " pdb=" OE1 GLU A 948 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR A 742 " pdb=" OP2 A B 30 " model vdw 2.247 2.440 nonbonded pdb="MG MG A1102 " pdb=" O3B ADP A1103 " model vdw 2.299 2.170 nonbonded pdb=" N GLU A 778 " pdb=" OE1 GLU A 778 " model vdw 2.314 2.520 ... (remaining 55466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.910 Find NCS groups from input model: 0.070 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 40.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.002 0.029 7027 Z= 0.122 Angle : 0.500 9.106 9774 Z= 0.242 Chirality : 0.034 0.147 1173 Planarity : 0.003 0.044 1037 Dihedral : 16.224 107.051 2981 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.80 % Allowed : 30.73 % Favored : 68.47 % 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: 2.43 (0.33), residues: 685 helix: 2.94 (0.27), residues: 340 sheet: 0.96 (0.65), residues: 75 loop : 0.08 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 734 HIS 0.003 0.000 HIS A 638 PHE 0.007 0.001 PHE A 762 TYR 0.008 0.001 TYR A 911 ARG 0.004 0.000 ARG A 868 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.713 Fit side-chains REVERT: A 702 THR cc_start: 0.8298 (m) cc_final: 0.8024 (p) REVERT: A 893 LYS cc_start: 0.8175 (tttt) cc_final: 0.7956 (mtpt) REVERT: A 1010 MET cc_start: 0.7787 (ttm) cc_final: 0.7102 (ttp) outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.8430 time to fit residues: 63.8105 Evaluate side-chains 61 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 992 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 506 ASN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7027 Z= 0.184 Angle : 0.504 6.139 9774 Z= 0.250 Chirality : 0.037 0.147 1173 Planarity : 0.003 0.039 1037 Dihedral : 11.082 58.504 1600 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.89 % Allowed : 24.84 % Favored : 69.27 % 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: 2.42 (0.33), residues: 685 helix: 2.94 (0.28), residues: 344 sheet: 1.06 (0.65), residues: 75 loop : -0.03 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 734 HIS 0.003 0.001 HIS A 331 PHE 0.011 0.001 PHE A 762 TYR 0.010 0.001 TYR A 911 ARG 0.004 0.000 ARG A1011 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 68 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.7745 (tpt) cc_final: 0.7437 (tpt) REVERT: A 865 ARG cc_start: 0.7450 (mmp-170) cc_final: 0.7169 (mmp-170) REVERT: A 1010 MET cc_start: 0.8135 (ttm) cc_final: 0.7922 (ttp) outliers start: 37 outliers final: 16 residues processed: 94 average time/residue: 0.7607 time to fit residues: 77.6302 Evaluate side-chains 81 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7027 Z= 0.189 Angle : 0.506 8.115 9774 Z= 0.245 Chirality : 0.036 0.153 1173 Planarity : 0.003 0.043 1037 Dihedral : 11.100 58.508 1598 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.46 % Allowed : 26.27 % Favored : 69.27 % 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: 2.32 (0.33), residues: 685 helix: 2.85 (0.27), residues: 345 sheet: 0.82 (0.64), residues: 73 loop : 0.00 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 989 HIS 0.004 0.001 HIS A 406 PHE 0.008 0.001 PHE A 346 TYR 0.011 0.001 TYR A 911 ARG 0.002 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 0.723 Fit side-chains REVERT: A 340 LYS cc_start: 0.7887 (tttt) cc_final: 0.7196 (ptmt) REVERT: A 454 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7045 (mtm) REVERT: A 477 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6308 (t70) REVERT: A 534 MET cc_start: 0.7844 (tpt) cc_final: 0.7502 (tpt) REVERT: A 544 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 609 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8146 (ttm170) REVERT: A 863 TRP cc_start: 0.3971 (OUTLIER) cc_final: 0.2445 (p90) REVERT: A 868 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8272 (mpt-90) REVERT: A 897 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 1010 MET cc_start: 0.8209 (ttm) cc_final: 0.7985 (ttp) outliers start: 28 outliers final: 9 residues processed: 84 average time/residue: 0.9688 time to fit residues: 87.2089 Evaluate side-chains 70 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7027 Z= 0.294 Angle : 0.561 7.000 9774 Z= 0.280 Chirality : 0.039 0.162 1173 Planarity : 0.004 0.039 1037 Dihedral : 11.242 58.988 1598 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.57 % Allowed : 25.16 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.33), residues: 685 helix: 2.43 (0.27), residues: 350 sheet: 0.38 (0.59), residues: 80 loop : -0.14 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 863 HIS 0.006 0.001 HIS A 406 PHE 0.012 0.002 PHE A 346 TYR 0.013 0.002 TYR A 911 ARG 0.005 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 51 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7374 (mtt) REVERT: A 519 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8399 (p0) REVERT: A 534 MET cc_start: 0.7782 (tpt) cc_final: 0.7442 (tpt) REVERT: A 543 MET cc_start: 0.7653 (mmm) cc_final: 0.7419 (mmt) REVERT: A 609 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8327 (ttm170) REVERT: A 661 MET cc_start: 0.8301 (tpt) cc_final: 0.8014 (tpt) REVERT: A 667 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8016 (ptp-170) REVERT: A 846 ASN cc_start: 0.8623 (t0) cc_final: 0.8412 (m-40) REVERT: A 863 TRP cc_start: 0.4423 (OUTLIER) cc_final: 0.3092 (p90) REVERT: A 921 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7559 (pp) REVERT: A 1010 MET cc_start: 0.8228 (ttm) cc_final: 0.7966 (ttp) outliers start: 35 outliers final: 16 residues processed: 80 average time/residue: 1.0387 time to fit residues: 88.3008 Evaluate side-chains 61 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 40 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1006 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7027 Z= 0.189 Angle : 0.526 9.783 9774 Z= 0.256 Chirality : 0.037 0.190 1173 Planarity : 0.003 0.028 1037 Dihedral : 11.257 58.529 1598 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.10 % Allowed : 25.80 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.33), residues: 685 helix: 2.52 (0.27), residues: 350 sheet: 0.28 (0.59), residues: 80 loop : -0.09 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 863 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 429 TYR 0.011 0.001 TYR A 911 ARG 0.002 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 50 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7405 (mtt) REVERT: A 534 MET cc_start: 0.7755 (tpt) cc_final: 0.7426 (tpt) REVERT: A 543 MET cc_start: 0.7671 (mmt) cc_final: 0.7310 (mmt) REVERT: A 544 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: A 609 ARG cc_start: 0.8642 (ttm170) cc_final: 0.8344 (ttm170) REVERT: A 661 MET cc_start: 0.8379 (tpt) cc_final: 0.8085 (tpt) REVERT: A 667 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8076 (ptp-170) REVERT: A 780 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8598 (mm) REVERT: A 863 TRP cc_start: 0.4215 (OUTLIER) cc_final: 0.2852 (p90) REVERT: A 865 ARG cc_start: 0.7510 (mmp-170) cc_final: 0.7246 (mmp-170) REVERT: A 921 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7521 (pp) REVERT: A 1010 MET cc_start: 0.8251 (ttm) cc_final: 0.8006 (ttp) REVERT: A 1011 ARG cc_start: 0.8584 (mmt180) cc_final: 0.8269 (mmp80) outliers start: 32 outliers final: 14 residues processed: 77 average time/residue: 1.0955 time to fit residues: 89.8143 Evaluate side-chains 62 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 42 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7027 Z= 0.303 Angle : 0.564 12.407 9774 Z= 0.282 Chirality : 0.038 0.164 1173 Planarity : 0.003 0.031 1037 Dihedral : 11.288 58.894 1598 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.25 % Allowed : 25.80 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.33), residues: 685 helix: 2.10 (0.28), residues: 363 sheet: 0.06 (0.58), residues: 80 loop : 0.09 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 863 HIS 0.004 0.001 HIS A 406 PHE 0.009 0.001 PHE A 346 TYR 0.012 0.001 TYR A 911 ARG 0.007 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 42 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8401 (p0) REVERT: A 534 MET cc_start: 0.7788 (tpt) cc_final: 0.7453 (tpt) REVERT: A 609 ARG cc_start: 0.8696 (ttm170) cc_final: 0.8377 (ttm170) REVERT: A 667 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8052 (ptp-170) REVERT: A 863 TRP cc_start: 0.4617 (OUTLIER) cc_final: 0.3022 (p90) REVERT: A 868 ARG cc_start: 0.8450 (mtt180) cc_final: 0.8227 (ptp-170) REVERT: A 921 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 1010 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7992 (ttp) outliers start: 33 outliers final: 16 residues processed: 69 average time/residue: 1.1460 time to fit residues: 84.0075 Evaluate side-chains 59 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1010 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7027 Z= 0.190 Angle : 0.537 13.198 9774 Z= 0.262 Chirality : 0.037 0.169 1173 Planarity : 0.003 0.029 1037 Dihedral : 11.296 58.489 1598 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.78 % Allowed : 26.59 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.33), residues: 685 helix: 2.27 (0.28), residues: 356 sheet: -0.07 (0.57), residues: 80 loop : 0.01 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 863 HIS 0.003 0.001 HIS A 638 PHE 0.008 0.001 PHE A 429 TYR 0.010 0.001 TYR A 911 ARG 0.004 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 42 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8420 (p0) REVERT: A 534 MET cc_start: 0.7728 (tpt) cc_final: 0.7401 (tpt) REVERT: A 609 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8380 (ttm170) REVERT: A 661 MET cc_start: 0.8639 (tpt) cc_final: 0.8416 (tpt) REVERT: A 667 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8586 (ttp-170) REVERT: A 780 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8723 (mm) REVERT: A 863 TRP cc_start: 0.4576 (OUTLIER) cc_final: 0.3068 (p90) REVERT: A 921 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7703 (pp) REVERT: A 1010 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7986 (ttp) outliers start: 30 outliers final: 15 residues processed: 68 average time/residue: 1.0017 time to fit residues: 72.7492 Evaluate side-chains 65 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 44 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7027 Z= 0.175 Angle : 0.536 9.890 9774 Z= 0.263 Chirality : 0.037 0.230 1173 Planarity : 0.003 0.030 1037 Dihedral : 11.264 58.451 1598 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.66 % Allowed : 27.71 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.33), residues: 685 helix: 2.33 (0.28), residues: 356 sheet: -0.09 (0.57), residues: 80 loop : -0.00 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 429 TYR 0.009 0.001 TYR A 911 ARG 0.003 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8402 (p0) REVERT: A 534 MET cc_start: 0.7705 (tpt) cc_final: 0.7380 (tpt) REVERT: A 609 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8374 (ttm170) REVERT: A 661 MET cc_start: 0.8657 (tpt) cc_final: 0.8383 (tpt) REVERT: A 764 ASP cc_start: 0.8325 (m-30) cc_final: 0.8106 (m-30) REVERT: A 780 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8717 (mm) REVERT: A 865 ARG cc_start: 0.7550 (mmp-170) cc_final: 0.6981 (mmp-170) REVERT: A 868 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8288 (mtt180) REVERT: A 921 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7699 (pp) REVERT: A 1010 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7985 (ttp) outliers start: 23 outliers final: 13 residues processed: 64 average time/residue: 1.0865 time to fit residues: 74.0359 Evaluate side-chains 58 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 71 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7027 Z= 0.209 Angle : 0.559 10.255 9774 Z= 0.271 Chirality : 0.037 0.231 1173 Planarity : 0.003 0.032 1037 Dihedral : 11.254 58.501 1598 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.66 % Allowed : 27.55 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.33), residues: 685 helix: 2.20 (0.27), residues: 362 sheet: 0.12 (0.62), residues: 70 loop : 0.15 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 734 HIS 0.003 0.001 HIS A 461 PHE 0.009 0.001 PHE A 429 TYR 0.010 0.001 TYR A 911 ARG 0.003 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8054 (tttt) cc_final: 0.7817 (tptm) REVERT: A 519 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8443 (p0) REVERT: A 534 MET cc_start: 0.7702 (tpt) cc_final: 0.7425 (tpt) REVERT: A 609 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8364 (ttm170) REVERT: A 764 ASP cc_start: 0.8320 (m-30) cc_final: 0.8100 (m-30) REVERT: A 780 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (mm) REVERT: A 921 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7722 (pp) REVERT: A 1010 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7978 (ttp) outliers start: 23 outliers final: 15 residues processed: 60 average time/residue: 1.0231 time to fit residues: 65.6523 Evaluate side-chains 62 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7027 Z= 0.195 Angle : 0.557 11.689 9774 Z= 0.270 Chirality : 0.037 0.217 1173 Planarity : 0.003 0.032 1037 Dihedral : 11.267 58.491 1598 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.03 % Allowed : 28.18 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.33), residues: 685 helix: 2.19 (0.27), residues: 362 sheet: 0.06 (0.61), residues: 70 loop : 0.13 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.008 0.001 PHE A 429 TYR 0.010 0.001 TYR A 911 ARG 0.002 0.000 ARG A 868 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8435 (p0) REVERT: A 609 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8352 (ttm170) REVERT: A 764 ASP cc_start: 0.8316 (m-30) cc_final: 0.8096 (m-30) REVERT: A 780 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8691 (mm) REVERT: A 921 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7711 (pp) REVERT: A 1010 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7993 (ttp) outliers start: 19 outliers final: 14 residues processed: 60 average time/residue: 1.0576 time to fit residues: 68.1452 Evaluate side-chains 60 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1010 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** 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 = 0.3563 r_free = 0.3563 target = 0.092045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067006 restraints weight = 14117.421| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.83 r_work: 0.2957 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7027 Z= 0.199 Angle : 0.574 11.495 9774 Z= 0.275 Chirality : 0.037 0.204 1173 Planarity : 0.003 0.032 1037 Dihedral : 11.272 58.502 1598 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.82 % Allowed : 27.71 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.33), residues: 685 helix: 2.19 (0.27), residues: 362 sheet: 0.04 (0.61), residues: 70 loop : 0.11 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.008 0.001 PHE A 429 TYR 0.010 0.001 TYR A 911 ARG 0.003 0.000 ARG A 865 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.81 seconds wall clock time: 38 minutes 53.56 seconds (2333.56 seconds total)