Starting phenix.real_space_refine on Thu Nov 14 06:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/11_2024/8sym_40884.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/11_2024/8sym_40884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/11_2024/8sym_40884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/11_2024/8sym_40884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/11_2024/8sym_40884.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/11_2024/8sym_40884.cif" } resolution = 3.2 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 2878 2.51 5 N 772 2.21 5 O 809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4486 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3023 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1463 Classifications: {'peptide': 184} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175} Time building chain proxies: 3.80, per 1000 atoms: 0.85 Number of scatterers: 4486 At special positions: 0 Unit cell: (76.4928, 89.2416, 74.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 809 8.00 N 772 7.00 C 2878 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 - 3.00 Amino acid : True - 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: 1.35 Conformation dependent library (CDL) restraints added in 671.4 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1066 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 54.8% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 582 through 597 removed outlier: 4.084A pdb=" N CYS A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.819A pdb=" N MET A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 Processing helix chain 'A' and resid 667 through 689 removed outlier: 3.552A pdb=" N LEU A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.998A pdb=" N ALA A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 717 through 734 Processing helix chain 'A' and resid 737 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 768 through 783 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 815 through 832 removed outlier: 3.642A pdb=" N HIS A 826 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 853 through 882 Processing helix chain 'A' and resid 883 through 902 removed outlier: 3.653A pdb=" N GLN A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 923 removed outlier: 3.820A pdb=" N HIS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 30 removed outlier: 3.576A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.729A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.940A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.463A pdb=" N LEU B 6 " --> pdb=" O HIS B 37 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 39 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 8 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81 264 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.55 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: 1460 1.34 - 1.46: 861 1.46 - 1.57: 2224 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4585 Sorted by residual: bond pdb=" C GLN B 93 " pdb=" N VAL B 94 " ideal model delta sigma weight residual 1.333 1.321 0.012 1.20e-02 6.94e+03 1.03e+00 bond pdb=" CB VAL B 112 " pdb=" CG2 VAL B 112 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.46e-01 bond pdb=" CG1 ILE A 805 " pdb=" CD1 ILE A 805 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 7.90e-01 bond pdb=" N VAL B 63 " pdb=" CA VAL B 63 " ideal model delta sigma weight residual 1.454 1.444 0.010 1.28e-02 6.10e+03 5.91e-01 bond pdb=" CA HIS A 901 " pdb=" CB HIS A 901 " ideal model delta sigma weight residual 1.537 1.524 0.012 1.67e-02 3.59e+03 5.37e-01 ... (remaining 4580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 6045 1.42 - 2.84: 129 2.84 - 4.26: 19 4.26 - 5.68: 5 5.68 - 7.10: 3 Bond angle restraints: 6201 Sorted by residual: angle pdb=" C LEU B 44 " pdb=" N CYS B 45 " pdb=" CA CYS B 45 " ideal model delta sigma weight residual 121.54 128.64 -7.10 1.91e+00 2.74e-01 1.38e+01 angle pdb=" C VAL A 752 " pdb=" CA VAL A 752 " pdb=" CB VAL A 752 " ideal model delta sigma weight residual 113.70 110.33 3.37 9.50e-01 1.11e+00 1.26e+01 angle pdb=" N GLY B 118 " pdb=" CA GLY B 118 " pdb=" C GLY B 118 " ideal model delta sigma weight residual 113.18 120.08 -6.90 2.37e+00 1.78e-01 8.47e+00 angle pdb=" C ALA A 900 " pdb=" N HIS A 901 " pdb=" CA HIS A 901 " ideal model delta sigma weight residual 122.42 118.86 3.56 1.77e+00 3.19e-01 4.03e+00 angle pdb=" C LEU A 751 " pdb=" N VAL A 752 " pdb=" CA VAL A 752 " ideal model delta sigma weight residual 120.43 122.23 -1.80 9.60e-01 1.09e+00 3.51e+00 ... (remaining 6196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2466 16.30 - 32.61: 218 32.61 - 48.91: 57 48.91 - 65.21: 4 65.21 - 81.52: 6 Dihedral angle restraints: 2751 sinusoidal: 1110 harmonic: 1641 Sorted by residual: dihedral pdb=" CA MET A 689 " pdb=" C MET A 689 " pdb=" N LYS A 690 " pdb=" CA LYS A 690 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA HIS A 33 " pdb=" C HIS A 33 " pdb=" N PRO A 34 " pdb=" CA PRO A 34 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TYR A 32 " pdb=" C TYR A 32 " pdb=" N HIS A 33 " pdb=" CA HIS A 33 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 443 0.034 - 0.068: 168 0.068 - 0.101: 57 0.101 - 0.135: 30 0.135 - 0.169: 2 Chirality restraints: 700 Sorted by residual: chirality pdb=" CB ILE A 718 " pdb=" CA ILE A 718 " pdb=" CG1 ILE A 718 " pdb=" CG2 ILE A 718 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 761 " pdb=" N ILE A 761 " pdb=" C ILE A 761 " pdb=" CB ILE A 761 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 697 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 15 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 16 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 712 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 713 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 713 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 713 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 33 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 34 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " -0.017 5.00e-02 4.00e+02 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 948 2.78 - 3.31: 4419 3.31 - 3.84: 7481 3.84 - 4.37: 8784 4.37 - 4.90: 14699 Nonbonded interactions: 36331 Sorted by model distance: nonbonded pdb=" NE2 GLN A 806 " pdb=" OH TYR A 821 " model vdw 2.253 3.120 nonbonded pdb=" NH1 ARG A 11 " pdb=" OD1 ASP B 99 " model vdw 2.301 3.120 nonbonded pdb=" O PRO A 756 " pdb=" OG SER A 768 " model vdw 2.322 3.040 nonbonded pdb=" NH2 ARG A 11 " pdb=" OE1 GLU A 16 " model vdw 2.356 3.120 nonbonded pdb=" NE2 HIS A 839 " pdb=" OD2 ASP A 847 " model vdw 2.357 3.120 ... (remaining 36326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.590 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.340 Find NCS groups from input model: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.004 0.035 4585 Z= 0.287 Angle : 0.542 7.096 6201 Z= 0.301 Chirality : 0.044 0.169 700 Planarity : 0.004 0.042 790 Dihedral : 13.673 81.517 1685 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.35), residues: 552 helix: 1.99 (0.31), residues: 289 sheet: 1.00 (0.69), residues: 61 loop : 0.13 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 6 HIS 0.007 0.001 HIS A 33 PHE 0.013 0.002 PHE A 744 TYR 0.011 0.002 TYR A 725 ARG 0.002 0.000 ARG A 686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 598 GLN cc_start: 0.8058 (mp-120) cc_final: 0.7788 (mm-40) REVERT: A 602 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8065 (mtpp) REVERT: A 642 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7654 (ttmm) REVERT: A 661 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7639 (tmm-80) REVERT: A 679 ASN cc_start: 0.7791 (m-40) cc_final: 0.7147 (m-40) REVERT: A 696 LYS cc_start: 0.8158 (mttt) cc_final: 0.7949 (mttt) REVERT: A 825 LEU cc_start: 0.8791 (mt) cc_final: 0.8560 (mp) REVERT: A 855 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7184 (mtpt) REVERT: A 862 LYS cc_start: 0.8188 (tppt) cc_final: 0.7735 (tppt) REVERT: A 881 ASP cc_start: 0.7609 (m-30) cc_final: 0.7285 (m-30) REVERT: A 894 PHE cc_start: 0.8616 (t80) cc_final: 0.8137 (t80) REVERT: A 911 GLN cc_start: 0.7991 (tp40) cc_final: 0.7463 (tp40) REVERT: A 915 ASN cc_start: 0.8247 (m-40) cc_final: 0.7572 (m110) REVERT: B 105 LEU cc_start: 0.8363 (mp) cc_final: 0.8097 (mm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2245 time to fit residues: 39.9992 Evaluate side-chains 139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.0060 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN A 666 ASN A 673 GLN A 806 GLN A 813 ASN ** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 911 GLN B 4 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4585 Z= 0.232 Angle : 0.526 6.891 6201 Z= 0.280 Chirality : 0.043 0.184 700 Planarity : 0.004 0.042 790 Dihedral : 4.506 17.356 598 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.35), residues: 552 helix: 1.94 (0.30), residues: 296 sheet: 0.86 (0.69), residues: 61 loop : 0.22 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.005 0.001 HIS A 33 PHE 0.014 0.002 PHE A 779 TYR 0.008 0.001 TYR A 707 ARG 0.003 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7196 (mt-10) REVERT: A 598 GLN cc_start: 0.8002 (mp-120) cc_final: 0.7799 (mm-40) REVERT: A 602 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8067 (mtpp) REVERT: A 642 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7656 (ttmm) REVERT: A 673 GLN cc_start: 0.8415 (tp40) cc_final: 0.8202 (tp40) REVERT: A 679 ASN cc_start: 0.7887 (m-40) cc_final: 0.7640 (m110) REVERT: A 684 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 696 LYS cc_start: 0.8065 (mttt) cc_final: 0.7860 (mttt) REVERT: A 825 LEU cc_start: 0.8875 (mt) cc_final: 0.8524 (mp) REVERT: A 855 LYS cc_start: 0.7475 (mtpt) cc_final: 0.7038 (mtpt) REVERT: A 862 LYS cc_start: 0.8230 (tppt) cc_final: 0.7770 (tppt) REVERT: A 881 ASP cc_start: 0.7533 (m-30) cc_final: 0.7181 (m-30) REVERT: A 894 PHE cc_start: 0.8626 (t80) cc_final: 0.8224 (t80) REVERT: B 34 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7901 (mtpt) REVERT: B 105 LEU cc_start: 0.8422 (mp) cc_final: 0.8159 (mm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2424 time to fit residues: 39.3007 Evaluate side-chains 132 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 49 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN A 813 ASN ** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4585 Z= 0.228 Angle : 0.519 6.424 6201 Z= 0.278 Chirality : 0.043 0.185 700 Planarity : 0.004 0.042 790 Dihedral : 4.468 16.920 598 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.60 % Allowed : 15.43 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.35), residues: 552 helix: 1.90 (0.30), residues: 297 sheet: 0.79 (0.67), residues: 61 loop : 0.29 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 6 HIS 0.005 0.001 HIS A 33 PHE 0.014 0.001 PHE A 779 TYR 0.008 0.001 TYR A 808 ARG 0.004 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 642 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7672 (ttmm) REVERT: A 684 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7101 (mt-10) REVERT: A 855 LYS cc_start: 0.7372 (mtpt) cc_final: 0.7085 (mtpt) REVERT: A 862 LYS cc_start: 0.8259 (tppt) cc_final: 0.7743 (tppt) REVERT: A 881 ASP cc_start: 0.7519 (m-30) cc_final: 0.7169 (m-30) REVERT: A 894 PHE cc_start: 0.8636 (t80) cc_final: 0.8262 (t80) REVERT: B 105 LEU cc_start: 0.8414 (mp) cc_final: 0.8134 (mm) REVERT: B 168 VAL cc_start: 0.8457 (t) cc_final: 0.7983 (m) outliers start: 3 outliers final: 1 residues processed: 139 average time/residue: 0.2482 time to fit residues: 41.0696 Evaluate side-chains 139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN B 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4585 Z= 0.343 Angle : 0.576 7.234 6201 Z= 0.304 Chirality : 0.045 0.169 700 Planarity : 0.004 0.041 790 Dihedral : 4.608 18.550 598 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.80 % Allowed : 16.23 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.61 (0.35), residues: 552 helix: 1.79 (0.30), residues: 296 sheet: 0.61 (0.67), residues: 61 loop : 0.23 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 97 HIS 0.009 0.001 HIS A 33 PHE 0.022 0.002 PHE A 779 TYR 0.014 0.001 TYR A 808 ARG 0.004 0.001 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 642 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7701 (ttmm) REVERT: A 679 ASN cc_start: 0.7893 (m-40) cc_final: 0.7592 (m110) REVERT: A 684 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 765 MET cc_start: 0.7881 (mmm) cc_final: 0.6952 (mmm) REVERT: A 806 GLN cc_start: 0.7804 (tp40) cc_final: 0.7336 (tp-100) REVERT: A 855 LYS cc_start: 0.7424 (mtpt) cc_final: 0.7128 (mtpt) REVERT: A 862 LYS cc_start: 0.8259 (tppt) cc_final: 0.7787 (tppt) REVERT: A 881 ASP cc_start: 0.7540 (m-30) cc_final: 0.7189 (m-30) REVERT: A 894 PHE cc_start: 0.8658 (t80) cc_final: 0.8242 (t80) REVERT: B 105 LEU cc_start: 0.8454 (mp) cc_final: 0.8171 (mm) REVERT: B 168 VAL cc_start: 0.8492 (t) cc_final: 0.8038 (m) outliers start: 9 outliers final: 6 residues processed: 143 average time/residue: 0.2412 time to fit residues: 40.8885 Evaluate side-chains 147 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.4980 chunk 30 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4585 Z= 0.235 Angle : 0.527 6.636 6201 Z= 0.281 Chirality : 0.043 0.146 700 Planarity : 0.004 0.042 790 Dihedral : 4.508 18.116 598 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.20 % Allowed : 17.64 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.65 (0.35), residues: 552 helix: 1.79 (0.30), residues: 297 sheet: 0.59 (0.67), residues: 61 loop : 0.32 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 6 HIS 0.005 0.001 HIS A 33 PHE 0.012 0.001 PHE A 779 TYR 0.010 0.001 TYR A 808 ARG 0.003 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 642 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7709 (ttmm) REVERT: A 679 ASN cc_start: 0.7859 (m-40) cc_final: 0.7593 (m110) REVERT: A 684 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7185 (mt-10) REVERT: A 765 MET cc_start: 0.7853 (mmm) cc_final: 0.6959 (mmm) REVERT: A 806 GLN cc_start: 0.7806 (tp40) cc_final: 0.7349 (tp-100) REVERT: A 862 LYS cc_start: 0.8245 (tppt) cc_final: 0.7777 (tppt) REVERT: A 894 PHE cc_start: 0.8635 (t80) cc_final: 0.8243 (t80) REVERT: B 105 LEU cc_start: 0.8458 (mp) cc_final: 0.8184 (mm) REVERT: B 168 VAL cc_start: 0.8493 (t) cc_final: 0.8006 (m) outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.2452 time to fit residues: 37.9598 Evaluate side-chains 133 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4585 Z= 0.320 Angle : 0.580 7.550 6201 Z= 0.305 Chirality : 0.044 0.141 700 Planarity : 0.004 0.042 790 Dihedral : 4.619 19.621 598 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.40 % Allowed : 17.23 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.51 (0.35), residues: 552 helix: 1.68 (0.30), residues: 296 sheet: 0.52 (0.67), residues: 61 loop : 0.24 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 6 HIS 0.009 0.001 HIS A 33 PHE 0.017 0.001 PHE A 779 TYR 0.014 0.001 TYR A 808 ARG 0.004 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 642 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7732 (ttmm) REVERT: A 679 ASN cc_start: 0.7879 (m-40) cc_final: 0.7302 (m-40) REVERT: A 684 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 765 MET cc_start: 0.7843 (mmm) cc_final: 0.6919 (mmm) REVERT: A 806 GLN cc_start: 0.7849 (tp40) cc_final: 0.7363 (tp-100) REVERT: A 859 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7015 (mm-30) REVERT: A 862 LYS cc_start: 0.8265 (tppt) cc_final: 0.7800 (tppt) REVERT: A 894 PHE cc_start: 0.8639 (t80) cc_final: 0.8251 (t80) REVERT: B 105 LEU cc_start: 0.8440 (mp) cc_final: 0.8156 (mm) REVERT: B 168 VAL cc_start: 0.8526 (t) cc_final: 0.8047 (m) outliers start: 12 outliers final: 8 residues processed: 135 average time/residue: 0.2441 time to fit residues: 38.9153 Evaluate side-chains 139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 673 GLN ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4585 Z= 0.285 Angle : 0.570 6.918 6201 Z= 0.300 Chirality : 0.044 0.140 700 Planarity : 0.004 0.042 790 Dihedral : 4.629 19.766 598 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.20 % Allowed : 18.84 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.52 (0.36), residues: 552 helix: 1.67 (0.30), residues: 297 sheet: 0.63 (0.64), residues: 71 loop : 0.20 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.007 0.001 HIS A 33 PHE 0.013 0.001 PHE A 779 TYR 0.013 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7761 (ttmm) REVERT: A 679 ASN cc_start: 0.7857 (m-40) cc_final: 0.7592 (m110) REVERT: A 684 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 765 MET cc_start: 0.7824 (mmm) cc_final: 0.6974 (mmm) REVERT: A 859 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 862 LYS cc_start: 0.8234 (tppt) cc_final: 0.7798 (tppt) REVERT: A 894 PHE cc_start: 0.8639 (t80) cc_final: 0.8247 (t80) REVERT: B 34 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7811 (mtpt) REVERT: B 105 LEU cc_start: 0.8460 (mp) cc_final: 0.8176 (mm) REVERT: B 168 VAL cc_start: 0.8517 (t) cc_final: 0.8039 (m) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.2430 time to fit residues: 39.0354 Evaluate side-chains 139 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 673 GLN A 789 HIS ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4585 Z= 0.247 Angle : 0.546 6.740 6201 Z= 0.289 Chirality : 0.043 0.140 700 Planarity : 0.004 0.042 790 Dihedral : 4.571 20.072 598 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.40 % Allowed : 19.64 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.59 (0.36), residues: 552 helix: 1.72 (0.30), residues: 297 sheet: 0.63 (0.64), residues: 71 loop : 0.26 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 6 HIS 0.006 0.001 HIS A 33 PHE 0.011 0.001 PHE A 779 TYR 0.014 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7711 (mtpp) REVERT: A 679 ASN cc_start: 0.7856 (m-40) cc_final: 0.7600 (m110) REVERT: A 684 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 765 MET cc_start: 0.7903 (mmm) cc_final: 0.7001 (mmm) REVERT: A 859 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6939 (mm-30) REVERT: A 862 LYS cc_start: 0.8231 (tppt) cc_final: 0.7768 (tppt) REVERT: A 894 PHE cc_start: 0.8618 (t80) cc_final: 0.8240 (t80) REVERT: B 34 LYS cc_start: 0.8116 (ttpt) cc_final: 0.7819 (mtpt) REVERT: B 105 LEU cc_start: 0.8430 (mp) cc_final: 0.8150 (mm) REVERT: B 168 VAL cc_start: 0.8502 (t) cc_final: 0.8016 (m) outliers start: 7 outliers final: 7 residues processed: 133 average time/residue: 0.2584 time to fit residues: 40.3728 Evaluate side-chains 136 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.0050 chunk 21 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 673 GLN B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4585 Z= 0.182 Angle : 0.520 6.828 6201 Z= 0.275 Chirality : 0.041 0.141 700 Planarity : 0.004 0.041 790 Dihedral : 4.407 19.767 598 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.60 % Allowed : 19.44 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.36), residues: 552 helix: 1.93 (0.30), residues: 297 sheet: 0.69 (0.64), residues: 71 loop : 0.31 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 6 HIS 0.004 0.001 HIS A 33 PHE 0.015 0.001 PHE A 640 TYR 0.013 0.001 TYR A 808 ARG 0.006 0.001 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 618 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8195 (t-90) REVERT: A 679 ASN cc_start: 0.7843 (m-40) cc_final: 0.7602 (m110) REVERT: A 684 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7076 (mt-10) REVERT: A 765 MET cc_start: 0.7927 (mmm) cc_final: 0.7041 (mmm) REVERT: A 806 GLN cc_start: 0.7852 (tp40) cc_final: 0.7525 (tp40) REVERT: A 862 LYS cc_start: 0.8179 (tppt) cc_final: 0.7749 (tppt) REVERT: A 894 PHE cc_start: 0.8611 (t80) cc_final: 0.8205 (t80) REVERT: B 105 LEU cc_start: 0.8439 (mp) cc_final: 0.8162 (mm) REVERT: B 168 VAL cc_start: 0.8495 (t) cc_final: 0.8001 (m) outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.2462 time to fit residues: 40.4395 Evaluate side-chains 140 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 0.0980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4585 Z= 0.214 Angle : 0.542 6.428 6201 Z= 0.286 Chirality : 0.042 0.144 700 Planarity : 0.004 0.040 790 Dihedral : 4.408 20.514 598 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.40 % Allowed : 20.24 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.36), residues: 552 helix: 1.92 (0.30), residues: 297 sheet: 0.85 (0.64), residues: 69 loop : 0.26 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.005 0.001 HIS A 33 PHE 0.011 0.001 PHE B 154 TYR 0.013 0.001 TYR A 808 ARG 0.005 0.001 ARG A 695 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 618 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8204 (t-90) REVERT: A 679 ASN cc_start: 0.7842 (m-40) cc_final: 0.7598 (m110) REVERT: A 684 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 765 MET cc_start: 0.7924 (mmm) cc_final: 0.7021 (mmm) REVERT: A 806 GLN cc_start: 0.7825 (tp40) cc_final: 0.7521 (tp40) REVERT: A 862 LYS cc_start: 0.8179 (tppt) cc_final: 0.7727 (tppt) REVERT: A 894 PHE cc_start: 0.8609 (t80) cc_final: 0.8210 (t80) REVERT: B 34 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7739 (mtpt) REVERT: B 105 LEU cc_start: 0.8448 (mp) cc_final: 0.8172 (mm) REVERT: B 168 VAL cc_start: 0.8499 (t) cc_final: 0.8017 (m) outliers start: 7 outliers final: 6 residues processed: 134 average time/residue: 0.2485 time to fit residues: 39.3692 Evaluate side-chains 137 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 HIS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN A 673 GLN ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109565 restraints weight = 6703.337| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.23 r_work: 0.3302 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4585 Z= 0.312 Angle : 0.587 7.473 6201 Z= 0.311 Chirality : 0.044 0.156 700 Planarity : 0.004 0.038 790 Dihedral : 4.571 21.668 598 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.40 % Allowed : 20.64 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.66 (0.36), residues: 552 helix: 1.80 (0.30), residues: 297 sheet: 0.81 (0.64), residues: 69 loop : 0.20 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 6 HIS 0.009 0.001 HIS A 33 PHE 0.013 0.002 PHE A 779 TYR 0.015 0.001 TYR A 808 ARG 0.005 0.000 ARG A 695 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.75 seconds wall clock time: 30 minutes 19.13 seconds (1819.13 seconds total)