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/8sgj_40457.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.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=3.1 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8sgj_40457.map" } resolution = 3.1 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= 0.062 sd= 0.217 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 31 5.16 5 C 4953 2.51 5 N 1242 2.21 5 O 1444 1.98 5 H 7601 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 874": "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: 15271 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 11821 Inner-chain residues flagged as termini: ['pdbres="PRO A 248 "', 'pdbres="PRO A 370 "', 'pdbres="SER A 467 "', 'pdbres="THR A 482 "', 'pdbres="ALA A 644 "', 'pdbres="PRO A 652 "', 'pdbres="THR A 698 "', 'pdbres="ASN A 707 "', 'pdbres="THR A 718 "', 'pdbres="SER A 737 "'] Classifications: {'peptide': 751} Modifications used: {'COO': 6, 'NH2': 2, 'NH3': 4} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 724} Chain breaks: 5 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: 4.19, per 1000 atoms: 0.27 Number of scatterers: 15271 At special positions: 0 Unit cell: (98.77, 100.43, 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 31 16.00 O 1444 8.00 N 1242 7.00 C 4953 6.00 H 7601 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: 6.96 Conformation dependent library (CDL) restraints added in 1.2 seconds Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 35.1% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 37 through 71 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 130 through 154 removed outlier: 4.019A pdb=" N ILE A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 188 removed outlier: 3.737A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 4.520A 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 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 657 through 667 removed outlier: 3.629A pdb=" N GLY A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 738 through 756 removed outlier: 5.457A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 794 removed outlier: 5.984A pdb=" N ALA A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 768 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 770 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 771 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 772 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 773 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 776 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 782 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 783 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 784 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA A 787 " --> pdb=" O GLY A 784 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A 789 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 792 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 793 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.519A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 861 removed outlier: 4.055A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 894 removed outlier: 4.057A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 932 removed outlier: 3.785A pdb=" N TYR A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) 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 74 through 79 removed outlier: 4.332A pdb=" N TYR A 228 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.870A pdb=" N SER A 372 " --> pdb=" O CYS A 485 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 380 through 384 removed outlier: 7.828A pdb=" N TYR A 381 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 493 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N CYS A 383 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR A 495 " --> pdb=" O CYS A 383 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 504 through 507 Processing sheet with id= E, first strand: chain 'A' and resid 511 through 515 removed outlier: 7.932A pdb=" N THR A 512 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 678 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 514 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 680 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.860A pdb=" N ASN A 534 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 536 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU A 596 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 613 through 620 removed outlier: 4.119A pdb=" N VAL A 625 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS A 618 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 623 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.045A pdb=" N LYS L 104 " --> pdb=" O LEU L 9 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR L 106 " --> pdb=" O THR L 11 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN L 38 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS L 40 " --> pdb=" O PHE L 45 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE L 45 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 16 through 21 Processing sheet with id= J, first strand: chain 'L' and resid 90 through 92 Processing sheet with id= K, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= L, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.265A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 981 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: 5.19 Time building geometry restraints manager: 6.81 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: 7590 1.14 - 1.31: 1261 1.31 - 1.48: 3246 1.48 - 1.64: 3308 1.64 - 1.81: 45 Bond restraints: 15450 Sorted by residual: bond pdb=" N ASN L 54 " pdb=" H ASN L 54 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" N SER A 852 " pdb=" H SER A 852 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N ILE A 136 " pdb=" H ILE A 136 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" N GLY A 900 " pdb=" H GLY A 900 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N VAL A 812 " pdb=" H VAL A 812 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 15445 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 180 106.34 - 113.25: 18018 113.25 - 120.17: 4851 120.17 - 127.08: 4740 127.08 - 133.99: 89 Bond angle restraints: 27878 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 114.17 110.91 3.26 1.14e+00 7.69e-01 8.18e+00 angle pdb=" C GLU A 426 " pdb=" N GLY A 427 " pdb=" CA GLY A 427 " ideal model delta sigma weight residual 121.03 117.80 3.23 1.51e+00 4.39e-01 4.58e+00 angle pdb=" N GLY A 549 " pdb=" CA GLY A 549 " pdb=" C GLY A 549 " ideal model delta sigma weight residual 113.18 108.43 4.75 2.37e+00 1.78e-01 4.02e+00 angle pdb=" CA SER A 655 " pdb=" C SER A 655 " pdb=" N LYS A 656 " ideal model delta sigma weight residual 119.38 117.14 2.24 1.24e+00 6.50e-01 3.27e+00 angle pdb=" N GLY A 427 " pdb=" CA GLY A 427 " pdb=" C GLY A 427 " ideal model delta sigma weight residual 110.18 112.95 -2.77 1.56e+00 4.11e-01 3.15e+00 ... (remaining 27873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 4831 15.67 - 31.34: 424 31.34 - 47.00: 152 47.00 - 62.67: 74 62.67 - 78.34: 12 Dihedral angle restraints: 5493 sinusoidal: 3858 harmonic: 1635 Sorted by residual: 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 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LEU A 637 " pdb=" C LEU A 637 " pdb=" N SER A 638 " pdb=" CA SER A 638 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.52e+00 dihedral pdb=" CB LYS A 909 " pdb=" CG LYS A 909 " pdb=" CD LYS A 909 " pdb=" CE LYS A 909 " ideal model delta sinusoidal sigma weight residual -180.00 -125.72 -54.28 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 5490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 724 0.029 - 0.057: 329 0.057 - 0.086: 82 0.086 - 0.114: 54 0.114 - 0.142: 28 Chirality restraints: 1217 Sorted by residual: chirality pdb=" CA ILE A 520 " pdb=" N ILE A 520 " pdb=" C ILE A 520 " pdb=" CB ILE A 520 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA VAL A 430 " pdb=" N VAL A 430 " pdb=" C VAL A 430 " pdb=" CB VAL A 430 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 1214 not shown) Planarity restraints: 2283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 133 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 112 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 52 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO H 53 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " -0.019 5.00e-02 4.00e+02 ... (remaining 2280 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 558 2.06 - 2.70: 21970 2.70 - 3.33: 43724 3.33 - 3.97: 59518 3.97 - 4.60: 88015 Nonbonded interactions: 213785 Sorted by model distance: nonbonded pdb=" OD1 ASP A 408 " pdb=" HG1 THR A 428 " model vdw 1.429 1.850 nonbonded pdb=" OE1 GLN H 35 " pdb=" HE1 TRP H 47 " model vdw 1.526 1.850 nonbonded pdb="HH21 ARG A 396 " pdb=" O ASP A 435 " model vdw 1.532 1.850 nonbonded pdb=" O PHE A 613 " pdb=" H ILE A 641 " model vdw 1.534 1.850 nonbonded pdb="HD21 ASN A 534 " pdb=" OE1 GLN A 563 " model vdw 1.537 1.850 ... (remaining 213780 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: 0.090 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: 0.150 Extract box with map and model: 0.420 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 29.050 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:21.770 Internal consistency checks: 0.000 Total: 51.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7849 Z= 0.139 Angle : 0.473 4.750 10661 Z= 0.265 Chirality : 0.042 0.142 1217 Planarity : 0.004 0.045 1340 Dihedral : 11.934 78.340 2758 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 0.12 % Allowed : 0.97 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.33 (0.25), residues: 966 helix: 0.03 (0.25), residues: 341 sheet: 0.02 (0.29), residues: 303 loop : -0.47 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.011 0.001 TYR H 60 PHE 0.011 0.001 PHE A 925 TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS A 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7849 Z= 0.156 Angle : 0.412 4.678 10661 Z= 0.223 Chirality : 0.052 0.172 1217 Planarity : 0.003 0.033 1340 Dihedral : 10.684 76.204 2758 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.04 % Favored : 95.65 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.22 (0.25), residues: 966 helix: -0.52 (0.24), residues: 337 sheet: -0.54 (0.28), residues: 303 loop : -1.10 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.007 0.001 TYR H 52 PHE 0.009 0.001 PHE A 587 TRP 0.007 0.001 TRP A 709 HIS 0.002 0.001 HIS A 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7849 Z= 0.464 Angle : 0.578 5.922 10661 Z= 0.322 Chirality : 0.059 0.217 1217 Planarity : 0.004 0.041 1340 Dihedral : 11.268 83.297 2758 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 1.24 % Allowed : 6.11 % Favored : 92.65 % Rotamer: Outliers : 0.24 % Allowed : 1.93 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.99 (0.23), residues: 966 helix: -1.39 (0.24), residues: 343 sheet: -1.78 (0.27), residues: 293 loop : -2.54 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 13 TYR 0.013 0.002 TYR H 52 PHE 0.015 0.002 PHE A 879 TRP 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS A 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7849 Z= 0.379 Angle : 0.496 5.093 10661 Z= 0.275 Chirality : 0.056 0.190 1217 Planarity : 0.004 0.036 1340 Dihedral : 11.131 88.489 2758 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 1.66 % Allowed : 6.63 % Favored : 91.72 % Rotamer: Outliers : 0.48 % Allowed : 3.26 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.16 (0.23), residues: 966 helix: -1.41 (0.24), residues: 345 sheet: -2.04 (0.28), residues: 292 loop : -2.60 (0.28), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 13 TYR 0.013 0.002 TYR A 180 PHE 0.013 0.001 PHE A 456 TRP 0.013 0.002 TRP A 709 HIS 0.004 0.001 HIS A 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 26 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 7849 Z= 0.514 Angle : 0.569 5.686 10661 Z= 0.317 Chirality : 0.059 0.198 1217 Planarity : 0.004 0.045 1340 Dihedral : 11.615 86.385 2758 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 1.76 % Allowed : 9.21 % Favored : 89.03 % Rotamer: Outliers : 1.21 % Allowed : 3.38 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.76 (0.23), residues: 966 helix: -1.80 (0.23), residues: 343 sheet: -2.44 (0.27), residues: 292 loop : -2.99 (0.27), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 13 TYR 0.013 0.002 TYR L 93 PHE 0.015 0.002 PHE A 879 TRP 0.015 0.002 TRP A 709 HIS 0.004 0.001 HIS A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7849 Z= 0.316 Angle : 0.461 4.901 10661 Z= 0.252 Chirality : 0.054 0.184 1217 Planarity : 0.004 0.034 1340 Dihedral : 11.074 84.252 2758 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 1.55 % Allowed : 7.66 % Favored : 90.79 % Rotamer: Outliers : 1.33 % Allowed : 3.38 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.39 (0.23), residues: 966 helix: -1.43 (0.24), residues: 345 sheet: -2.35 (0.27), residues: 285 loop : -2.74 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.011 0.001 TYR A 180 PHE 0.011 0.001 PHE A 587 TRP 0.010 0.001 TRP A 709 HIS 0.002 0.001 HIS A 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 364.28 seconds wall clock time: 6 minutes 58.54 seconds (418.54 seconds total)