Starting phenix.real_space_refine on Sun May 19 16:32:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.6 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgt_40467.map" } resolution = 3.6 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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= 0.056 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 4608 2.51 5 N 1145 2.21 5 O 1347 1.98 5 H 7044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 874": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 14174 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 10724 Inner-chain residues flagged as termini: ['pdbres="SER A 73 "', 'pdbres="GLU A 97 "', 'pdbres="PHE A 223 "', 'pdbres="PRO A 370 "', 'pdbres="SER A 467 "', 'pdbres="THR A 482 "', 'pdbres="ALA A 644 "', 'pdbres="LEU A 653 "', 'pdbres="GLU A 683 "', 'pdbres="ASN A 707 "', 'pdbres="THR A 718 "', 'pdbres="SER A 737 "'] Classifications: {'peptide': 687} Modifications used: {'COO': 7, 'NH2': 1, 'NH3': 6} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 663} Chain breaks: 6 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1609 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 4.25, per 1000 atoms: 0.30 Number of scatterers: 14174 At special positions: 0 Unit cell: (121.18, 97.11, 146.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 1347 8.00 N 1145 7.00 C 4608 6.00 H 7044 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.01 Conformation dependent library (CDL) restraints added in 972.5 milliseconds Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 35.2% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 37 through 71 Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.578A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 130 through 154 removed outlier: 3.716A pdb=" N ILE A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 188 removed outlier: 3.851A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 4.375A pdb=" N PHE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 657 through 666 removed outlier: 3.713A pdb=" N MET A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 738 through 756 removed outlier: 5.341A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 794 removed outlier: 5.910A pdb=" N ALA A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS A 768 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 770 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 771 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 772 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 773 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 776 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 782 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 783 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 784 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A 787 " --> pdb=" O GLY A 784 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 789 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS A 792 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 793 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 794 " --> pdb=" O GLY A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 804 Processing helix chain 'A' and resid 806 through 810 Processing helix chain 'A' and resid 812 through 824 Processing helix chain 'A' and resid 829 through 844 removed outlier: 3.647A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 860 removed outlier: 3.857A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 894 removed outlier: 3.947A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 931 Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.810A pdb=" N SER A 372 " --> pdb=" O CYS A 485 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 382 through 384 removed outlier: 8.005A pdb=" N CYS A 383 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR A 495 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 492 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 454 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 505 through 507 Processing sheet with id= D, first strand: chain 'A' and resid 511 through 515 removed outlier: 8.362A pdb=" N THR A 512 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A 678 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL A 514 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 680 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 598 through 600 removed outlier: 3.634A pdb=" N VAL A 625 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS A 618 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG A 627 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 616 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.278A pdb=" N LYS L 104 " --> pdb=" O LEU L 9 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR L 106 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN L 38 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS L 40 " --> pdb=" O PHE L 45 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE L 45 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 17 through 21 Processing sheet with id= H, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= I, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.194A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 861 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: 5.40 Time building geometry restraints manager: 7.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 7033 1.14 - 1.31: 1178 1.31 - 1.48: 3024 1.48 - 1.65: 3062 1.65 - 1.81: 43 Bond restraints: 14340 Sorted by residual: bond pdb=" N GLY A 848 " pdb=" H GLY A 848 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N LEU A 457 " pdb=" H LEU A 457 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N ILE A 59 " pdb=" H ILE A 59 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" N VAL H 37 " pdb=" H VAL H 37 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N GLN A 826 " pdb=" H GLN A 826 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 ... (remaining 14335 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.04: 291 107.04 - 113.80: 16895 113.80 - 120.56: 4717 120.56 - 127.32: 3877 127.32 - 134.07: 82 Bond angle restraints: 25862 Sorted by residual: angle pdb=" N SER A 655 " pdb=" CA SER A 655 " pdb=" CB SER A 655 " ideal model delta sigma weight residual 114.17 111.16 3.01 1.14e+00 7.69e-01 6.98e+00 angle pdb=" C GLU L 39 " pdb=" N LYS L 40 " pdb=" CA LYS L 40 " ideal model delta sigma weight residual 121.92 125.16 -3.24 1.60e+00 3.91e-01 4.09e+00 angle pdb=" C GLU A 559 " pdb=" N LEU A 560 " pdb=" CA LEU A 560 " ideal model delta sigma weight residual 121.32 117.11 4.21 2.10e+00 2.27e-01 4.01e+00 angle pdb=" C THR A 654 " pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 126.45 123.15 3.30 1.77e+00 3.19e-01 3.48e+00 angle pdb=" CA ARG A 632 " pdb=" CB ARG A 632 " pdb=" CG ARG A 632 " ideal model delta sigma weight residual 114.10 117.51 -3.41 2.00e+00 2.50e-01 2.91e+00 ... (remaining 25857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 4512 16.74 - 33.49: 383 33.49 - 50.23: 130 50.23 - 66.98: 59 66.98 - 83.72: 14 Dihedral angle restraints: 5098 sinusoidal: 3565 harmonic: 1533 Sorted by residual: dihedral pdb=" CA GLU A 566 " pdb=" C GLU A 566 " pdb=" N ILE A 567 " pdb=" CA ILE A 567 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR H 60 " pdb=" C TYR H 60 " pdb=" N THR H 61 " pdb=" CA THR H 61 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 675 0.030 - 0.060: 314 0.060 - 0.090: 84 0.090 - 0.121: 51 0.121 - 0.151: 16 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA ILE A 542 " pdb=" N ILE A 542 " pdb=" C ILE A 542 " pdb=" CB ILE A 542 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE A 641 " pdb=" N ILE A 641 " pdb=" C ILE A 641 " pdb=" CB ILE A 641 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 374 " pdb=" N ILE A 374 " pdb=" C ILE A 374 " pdb=" CB ILE A 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1137 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 133 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 112 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 488 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 489 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.018 5.00e-02 4.00e+02 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 683 2.09 - 2.72: 21952 2.72 - 3.35: 39561 3.35 - 3.97: 54584 3.97 - 4.60: 79880 Nonbonded interactions: 196660 Sorted by model distance: nonbonded pdb=" O VAL A 430 " pdb=" HZ2 LYS A 438 " model vdw 1.468 1.850 nonbonded pdb=" OE1 GLU A 113 " pdb=" H GLU A 113 " model vdw 1.513 1.850 nonbonded pdb=" O THR A 135 " pdb=" HG SER A 139 " model vdw 1.517 1.850 nonbonded pdb=" O LEU A 55 " pdb=" HG SER A 58 " model vdw 1.526 1.850 nonbonded pdb=" O SER A 35 " pdb=" HZ2 LYS A 39 " model vdw 1.530 1.850 ... (remaining 196655 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.520 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 29.540 Find NCS groups from input model: 0.170 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:19.760 Internal consistency checks: 0.000 Total: 50.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 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 : 0.003 0.053 7296 Z= 0.163 Angle : 0.519 5.447 9920 Z= 0.289 Chirality : 0.042 0.151 1140 Planarity : 0.004 0.041 1249 Dihedral : 12.725 82.505 2534 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.26), residues: 900 helix: -0.14 (0.27), residues: 314 sheet: -0.53 (0.32), residues: 251 loop : -0.92 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 595 TYR 0.012 0.001 TYR A 180 PHE 0.016 0.002 PHE A 553 TRP 0.007 0.001 TRP A 198 HIS 0.002 0.001 HIS A 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7296 Z= 0.345 Angle : 0.562 4.905 9920 Z= 0.307 Chirality : 0.055 0.208 1140 Planarity : 0.004 0.049 1249 Dihedral : 11.599 85.295 2534 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.22 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.98 (0.26), residues: 900 helix: -0.66 (0.26), residues: 321 sheet: -1.54 (0.32), residues: 245 loop : -1.54 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 527 TYR 0.015 0.001 TYR L 33 PHE 0.013 0.001 PHE H 108 TRP 0.012 0.001 TRP H 36 HIS 0.004 0.001 HIS A 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 40.0000 chunk 64 optimal weight: 60.0000 chunk 17 optimal weight: 90.0000 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 60.0000 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 18 optimal weight: 50.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7296 Z= 0.321 Angle : 0.529 4.866 9920 Z= 0.288 Chirality : 0.056 0.218 1140 Planarity : 0.003 0.031 1249 Dihedral : 11.057 80.211 2534 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 1.67 % Allowed : 8.00 % Favored : 90.33 % Rotamer: Outliers : 0.65 % Allowed : 2.34 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.79 (0.25), residues: 900 helix: -0.59 (0.26), residues: 319 sheet: -2.30 (0.30), residues: 243 loop : -2.58 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.009 0.001 TYR H 60 PHE 0.015 0.001 PHE L 88 TRP 0.015 0.001 TRP H 111 HIS 0.003 0.001 HIS A 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 80.0000 chunk 9 optimal weight: 70.0000 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 100.0000 chunk 71 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 50.0000 chunk 40 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7296 Z= 0.317 Angle : 0.497 6.947 9920 Z= 0.269 Chirality : 0.053 0.182 1140 Planarity : 0.003 0.032 1249 Dihedral : 10.822 79.436 2534 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 1.89 % Allowed : 9.00 % Favored : 89.11 % Rotamer: Outliers : 0.65 % Allowed : 2.47 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.97 (0.26), residues: 900 helix: -0.67 (0.27), residues: 318 sheet: -2.40 (0.30), residues: 244 loop : -2.76 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 527 TYR 0.015 0.001 TYR L 33 PHE 0.010 0.001 PHE A 562 TRP 0.013 0.001 TRP H 36 HIS 0.004 0.001 HIS A 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 70.0000 chunk 56 optimal weight: 60.0000 chunk 66 optimal weight: 50.0000 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 50.0000 chunk 1 optimal weight: 80.0000 chunk 11 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 overall best weight: 16.9998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 7296 Z= 0.576 Angle : 0.686 7.486 9920 Z= 0.379 Chirality : 0.059 0.233 1140 Planarity : 0.004 0.041 1249 Dihedral : 12.143 83.712 2534 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 5.00 % Allowed : 11.78 % Favored : 83.22 % Rotamer: Outliers : 2.60 % Allowed : 5.33 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.24), residues: 900 helix: -1.22 (0.26), residues: 314 sheet: -3.15 (0.29), residues: 234 loop : -3.64 (0.26), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 668 TYR 0.017 0.002 TYR L 33 PHE 0.021 0.002 PHE L 45 TRP 0.020 0.002 TRP H 111 HIS 0.006 0.001 HIS A 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 90 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 90.0000 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 80.0000 chunk 24 optimal weight: 80.0000 overall best weight: 5.7590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7296 Z= 0.237 Angle : 0.462 6.034 9920 Z= 0.249 Chirality : 0.053 0.202 1140 Planarity : 0.003 0.023 1249 Dihedral : 11.249 76.844 2534 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 3.00 % Allowed : 9.56 % Favored : 87.44 % Rotamer: Outliers : 1.56 % Allowed : 4.94 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -3.29 (0.25), residues: 900 helix: -0.85 (0.26), residues: 316 sheet: -2.69 (0.30), residues: 240 loop : -2.93 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.008 0.001 TYR L 87 PHE 0.010 0.001 PHE L 45 TRP 0.012 0.001 TRP H 111 HIS 0.003 0.001 HIS A 513 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 348.55 seconds wall clock time: 6 minutes 43.40 seconds (403.40 seconds total)