Starting phenix.real_space_refine on Fri Mar 15 16:32:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/03_2024/8j9z_36120.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/03_2024/8j9z_36120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/03_2024/8j9z_36120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/03_2024/8j9z_36120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/03_2024/8j9z_36120.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9z_36120/03_2024/8j9z_36120.pdb" } resolution = 3.13 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= 0.046 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 50 5.16 5 C 7818 2.51 5 N 2086 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 524": "OE1" <-> "OE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A GLU 1061": "OE1" <-> "OE2" Residue "A ASP 1153": "OD1" <-> "OD2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 927": "OE1" <-> "OE2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B GLU 1061": "OE1" <-> "OE2" Residue "B ASP 1153": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12154 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Chain: "B" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Time building chain proxies: 6.53, per 1000 atoms: 0.54 Number of scatterers: 12154 At special positions: 0 Unit cell: (124.45, 116.85, 114, 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 50 16.00 O 2200 8.00 N 2086 7.00 C 7818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 2.1 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 52.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.859A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.904A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.617A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.566A pdb=" N ARG A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.820A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 806 through 814 removed outlier: 4.215A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.627A pdb=" N TRP A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 959 removed outlier: 4.114A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.623A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.828A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1093 removed outlier: 3.626A pdb=" N ALA A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.793A pdb=" N LEU A1126 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1134 through 1160 removed outlier: 3.536A pdb=" N GLN A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.859A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.904A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.616A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 656 through 664 removed outlier: 3.566A pdb=" N ARG B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.820A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 806 through 814 removed outlier: 4.216A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 removed outlier: 3.626A pdb=" N TRP B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 959 removed outlier: 4.113A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.623A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.829A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1093 removed outlier: 3.625A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1122 through 1127 removed outlier: 3.793A pdb=" N LEU B1126 " --> pdb=" O TYR B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1133 Processing helix chain 'B' and resid 1134 through 1160 removed outlier: 3.536A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419 removed outlier: 5.392A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.752A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.010A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.503A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419 removed outlier: 5.392A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.752A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 925 removed outlier: 6.011A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.503A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1728 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: 4.09 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3916 1.34 - 1.46: 2499 1.46 - 1.58: 5953 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12446 Sorted by residual: bond pdb=" CB PRO A1096 " pdb=" CG PRO A1096 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.67e+00 bond pdb=" CB PRO B1096 " pdb=" CG PRO B1096 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.62e+00 bond pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.11e-01 bond pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.84e-01 bond pdb=" CA LEU A1036 " pdb=" C LEU A1036 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.26e-01 ... (remaining 12441 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.04: 324 107.04 - 113.78: 6841 113.78 - 120.52: 4914 120.52 - 127.25: 4603 127.25 - 133.99: 134 Bond angle restraints: 16816 Sorted by residual: angle pdb=" CA GLU B 524 " pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " ideal model delta sigma weight residual 114.10 118.92 -4.82 2.00e+00 2.50e-01 5.82e+00 angle pdb=" CA GLU A 524 " pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " ideal model delta sigma weight residual 114.10 118.90 -4.80 2.00e+00 2.50e-01 5.75e+00 angle pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " pdb=" CD GLU A 524 " ideal model delta sigma weight residual 112.60 116.21 -3.61 1.70e+00 3.46e-01 4.51e+00 angle pdb=" CB GLU B 524 " pdb=" CG GLU B 524 " pdb=" CD GLU B 524 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.70e+00 3.46e-01 4.45e+00 angle pdb=" CA PRO A1096 " pdb=" N PRO A1096 " pdb=" CD PRO A1096 " ideal model delta sigma weight residual 112.00 109.52 2.48 1.40e+00 5.10e-01 3.15e+00 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6476 17.85 - 35.71: 732 35.71 - 53.56: 222 53.56 - 71.42: 26 71.42 - 89.27: 18 Dihedral angle restraints: 7474 sinusoidal: 3088 harmonic: 4386 Sorted by residual: dihedral pdb=" CB GLU B 658 " pdb=" CG GLU B 658 " pdb=" CD GLU B 658 " pdb=" OE1 GLU B 658 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 658 " pdb=" CG GLU A 658 " pdb=" CD GLU A 658 " pdb=" OE1 GLU A 658 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 970 " pdb=" CG GLU B 970 " pdb=" CD GLU B 970 " pdb=" OE1 GLU B 970 " ideal model delta sinusoidal sigma weight residual 0.00 -88.51 88.51 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1105 0.026 - 0.053: 463 0.053 - 0.079: 158 0.079 - 0.105: 65 0.105 - 0.132: 29 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA ILE B 707 " pdb=" N ILE B 707 " pdb=" C ILE B 707 " pdb=" CB ILE B 707 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 707 " pdb=" N ILE A 707 " pdb=" C ILE A 707 " pdb=" CB ILE A 707 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE A 780 " pdb=" N ILE A 780 " pdb=" C ILE A 780 " pdb=" CB ILE A 780 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1817 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 669 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO A 670 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 669 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 670 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 524 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" CD GLU B 524 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU B 524 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 524 " 0.010 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 349 2.72 - 3.27: 11554 3.27 - 3.81: 19877 3.81 - 4.36: 24111 4.36 - 4.90: 42538 Nonbonded interactions: 98429 Sorted by model distance: nonbonded pdb=" NH2 ARG B1049 " pdb=" O PRO B1105 " model vdw 2.177 2.520 nonbonded pdb=" NH2 ARG A1049 " pdb=" O PRO A1105 " model vdw 2.177 2.520 nonbonded pdb=" O VAL B 838 " pdb=" NH1 ARG B1039 " model vdw 2.250 2.520 nonbonded pdb=" O VAL A 838 " pdb=" NH1 ARG A1039 " model vdw 2.251 2.520 nonbonded pdb=" OD2 ASP A 818 " pdb=" NH2 ARG A1039 " model vdw 2.254 2.520 ... (remaining 98424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.360 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: 0.010 Extract box with map and model: 6.200 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.950 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 0.082 12446 Z= 0.147 Angle : 0.411 5.482 16816 Z= 0.220 Chirality : 0.037 0.132 1820 Planarity : 0.004 0.081 2142 Dihedral : 16.682 89.271 4662 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.15 % Allowed : 18.02 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.31 (0.23), residues: 1486 helix: 2.22 (0.20), residues: 704 sheet: -1.16 (0.34), residues: 230 loop : 0.11 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1189 HIS 0.002 0.000 HIS B 883 PHE 0.010 0.001 PHE A 649 TYR 0.012 0.001 TYR A 888 ARG 0.008 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.310 Fit side-chains REVERT: A 856 TRP cc_start: 0.7409 (m100) cc_final: 0.7134 (m100) REVERT: B 503 LYS cc_start: 0.7053 (tppt) cc_final: 0.6495 (ttmm) REVERT: B 701 ASP cc_start: 0.8363 (t70) cc_final: 0.8125 (t0) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.2448 time to fit residues: 51.2690 Evaluate side-chains 133 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 0.0570 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS B 903 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12446 Z= 0.171 Angle : 0.413 5.230 16816 Z= 0.216 Chirality : 0.038 0.133 1820 Planarity : 0.004 0.060 2142 Dihedral : 3.252 13.033 1662 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 17.71 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.30 (0.23), residues: 1486 helix: 2.20 (0.20), residues: 706 sheet: -1.05 (0.35), residues: 224 loop : 0.04 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.003 0.001 HIS A 789 PHE 0.011 0.001 PHE B 596 TYR 0.015 0.001 TYR B 888 ARG 0.007 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.332 Fit side-chains REVERT: A 416 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7614 (p0) REVERT: A 856 TRP cc_start: 0.7373 (m100) cc_final: 0.7094 (m100) REVERT: B 416 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7538 (p0) REVERT: B 542 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6832 (pp) REVERT: B 735 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: B 790 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 878 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8005 (ptpp) REVERT: B 1048 MET cc_start: 0.8542 (mtp) cc_final: 0.8140 (mmm) outliers start: 25 outliers final: 12 residues processed: 151 average time/residue: 0.2473 time to fit residues: 54.0014 Evaluate side-chains 147 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12446 Z= 0.200 Angle : 0.416 5.229 16816 Z= 0.218 Chirality : 0.038 0.133 1820 Planarity : 0.003 0.050 2142 Dihedral : 3.337 13.800 1662 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.37 % Allowed : 18.02 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.26 (0.23), residues: 1486 helix: 2.15 (0.20), residues: 708 sheet: -0.98 (0.36), residues: 212 loop : -0.04 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.003 0.001 HIS A 789 PHE 0.008 0.001 PHE A 739 TYR 0.016 0.001 TYR A 888 ARG 0.008 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.325 Fit side-chains REVERT: A 416 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 856 TRP cc_start: 0.7393 (m100) cc_final: 0.7111 (m100) REVERT: B 416 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7575 (p0) REVERT: B 542 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.6928 (pp) REVERT: B 701 ASP cc_start: 0.8174 (t70) cc_final: 0.7903 (t0) REVERT: B 878 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8029 (ptpp) outliers start: 31 outliers final: 18 residues processed: 162 average time/residue: 0.2279 time to fit residues: 54.6306 Evaluate side-chains 156 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN A 892 HIS ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 ASN B 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12446 Z= 0.280 Angle : 0.466 5.007 16816 Z= 0.244 Chirality : 0.040 0.142 1820 Planarity : 0.004 0.044 2142 Dihedral : 3.656 18.884 1662 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.74 % Allowed : 17.40 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.02 (0.23), residues: 1486 helix: 1.98 (0.20), residues: 716 sheet: -1.08 (0.36), residues: 212 loop : -0.22 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.005 0.001 HIS A 789 PHE 0.011 0.001 PHE B1191 TYR 0.013 0.001 TYR A 888 ARG 0.007 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 131 time to evaluate : 1.388 Fit side-chains REVERT: A 416 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7677 (p0) REVERT: A 927 GLU cc_start: 0.7739 (tp30) cc_final: 0.7448 (mm-30) REVERT: B 416 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7632 (p0) REVERT: B 521 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8332 (ttmm) REVERT: B 542 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7441 (pp) REVERT: B 682 VAL cc_start: 0.8207 (m) cc_final: 0.7885 (p) REVERT: B 701 ASP cc_start: 0.8232 (t70) cc_final: 0.7886 (t0) REVERT: B 878 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8122 (ptpp) REVERT: B 962 GLU cc_start: 0.7692 (tt0) cc_final: 0.7410 (tt0) REVERT: B 1048 MET cc_start: 0.8591 (mtp) cc_final: 0.8202 (mtp) outliers start: 49 outliers final: 31 residues processed: 167 average time/residue: 0.2247 time to fit residues: 55.6313 Evaluate side-chains 165 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 chunk 2 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12446 Z= 0.184 Angle : 0.417 5.242 16816 Z= 0.218 Chirality : 0.038 0.136 1820 Planarity : 0.003 0.042 2142 Dihedral : 3.509 19.430 1662 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.21 % Allowed : 18.09 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.13 (0.23), residues: 1486 helix: 2.07 (0.20), residues: 716 sheet: -1.09 (0.36), residues: 212 loop : -0.16 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.003 0.001 HIS B 789 PHE 0.010 0.001 PHE A 710 TYR 0.009 0.001 TYR A 946 ARG 0.008 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 416 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7672 (p0) REVERT: A 441 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 892 HIS cc_start: 0.6713 (m-70) cc_final: 0.6471 (m170) REVERT: A 927 GLU cc_start: 0.7755 (tp30) cc_final: 0.7451 (mm-30) REVERT: A 1156 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: B 416 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7650 (p0) REVERT: B 521 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8316 (ttmm) REVERT: B 701 ASP cc_start: 0.8203 (t70) cc_final: 0.7881 (t0) REVERT: B 878 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8143 (ptpp) REVERT: B 962 GLU cc_start: 0.7674 (tt0) cc_final: 0.7392 (tt0) REVERT: B 1048 MET cc_start: 0.8579 (mtp) cc_final: 0.8211 (mtp) outliers start: 42 outliers final: 29 residues processed: 167 average time/residue: 0.2236 time to fit residues: 55.3630 Evaluate side-chains 164 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12446 Z= 0.268 Angle : 0.456 5.886 16816 Z= 0.237 Chirality : 0.039 0.144 1820 Planarity : 0.004 0.043 2142 Dihedral : 3.643 21.665 1662 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.44 % Allowed : 18.02 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.99 (0.23), residues: 1486 helix: 1.96 (0.20), residues: 716 sheet: -1.15 (0.36), residues: 212 loop : -0.24 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.004 0.001 HIS B 789 PHE 0.010 0.001 PHE B1191 TYR 0.010 0.001 TYR A 769 ARG 0.009 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 133 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 416 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7638 (p0) REVERT: A 441 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8080 (p) REVERT: A 701 ASP cc_start: 0.8177 (t70) cc_final: 0.7925 (t0) REVERT: A 892 HIS cc_start: 0.6725 (m-70) cc_final: 0.6426 (m170) REVERT: A 927 GLU cc_start: 0.7730 (tp30) cc_final: 0.7413 (mm-30) REVERT: A 1156 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7408 (tp30) REVERT: B 416 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7634 (p0) REVERT: B 441 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 521 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8411 (ttmm) REVERT: B 701 ASP cc_start: 0.8223 (t70) cc_final: 0.7864 (t0) REVERT: B 878 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8111 (ptpp) REVERT: B 1048 MET cc_start: 0.8567 (mtp) cc_final: 0.8215 (mtp) REVERT: B 1156 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7341 (tt0) outliers start: 45 outliers final: 34 residues processed: 165 average time/residue: 0.2265 time to fit residues: 55.4734 Evaluate side-chains 173 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12446 Z= 0.260 Angle : 0.451 4.881 16816 Z= 0.236 Chirality : 0.039 0.143 1820 Planarity : 0.004 0.046 2142 Dihedral : 3.677 24.174 1662 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.36 % Allowed : 18.24 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.97 (0.23), residues: 1486 helix: 1.94 (0.20), residues: 716 sheet: -0.92 (0.37), residues: 192 loop : -0.39 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.004 0.001 HIS B 789 PHE 0.010 0.001 PHE B 710 TYR 0.009 0.001 TYR A 769 ARG 0.009 0.000 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 416 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7618 (p0) REVERT: A 441 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (p) REVERT: A 701 ASP cc_start: 0.8189 (t70) cc_final: 0.7923 (t0) REVERT: A 927 GLU cc_start: 0.7731 (tp30) cc_final: 0.7437 (mm-30) REVERT: A 1156 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: B 416 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7629 (p0) REVERT: B 441 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8114 (p) REVERT: B 521 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8449 (ttmm) REVERT: B 701 ASP cc_start: 0.8228 (t70) cc_final: 0.7885 (t0) REVERT: B 878 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8120 (ptpp) REVERT: B 927 GLU cc_start: 0.7780 (tp30) cc_final: 0.7539 (mm-30) REVERT: B 1156 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7323 (tp30) outliers start: 44 outliers final: 29 residues processed: 168 average time/residue: 0.2246 time to fit residues: 56.0212 Evaluate side-chains 167 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12446 Z= 0.219 Angle : 0.433 5.324 16816 Z= 0.227 Chirality : 0.038 0.139 1820 Planarity : 0.004 0.042 2142 Dihedral : 3.614 24.253 1662 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.05 % Allowed : 18.55 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.01 (0.23), residues: 1486 helix: 1.99 (0.20), residues: 716 sheet: -1.23 (0.35), residues: 218 loop : -0.19 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS A 789 PHE 0.011 0.001 PHE B 710 TYR 0.016 0.001 TYR B 555 ARG 0.010 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7613 (p0) REVERT: A 441 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.8080 (p) REVERT: A 701 ASP cc_start: 0.8187 (t70) cc_final: 0.7937 (t0) REVERT: A 1156 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: B 416 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7617 (p0) REVERT: B 441 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 521 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8446 (ttmm) REVERT: B 682 VAL cc_start: 0.8072 (m) cc_final: 0.7733 (p) REVERT: B 701 ASP cc_start: 0.8227 (t70) cc_final: 0.7898 (t0) REVERT: B 878 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8095 (ptpp) REVERT: B 927 GLU cc_start: 0.7757 (tp30) cc_final: 0.7524 (mm-30) REVERT: B 1048 MET cc_start: 0.8605 (mtp) cc_final: 0.8267 (mtt) REVERT: B 1156 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7393 (tt0) outliers start: 40 outliers final: 29 residues processed: 163 average time/residue: 0.2279 time to fit residues: 54.5661 Evaluate side-chains 169 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 140 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12446 Z= 0.163 Angle : 0.417 5.854 16816 Z= 0.218 Chirality : 0.038 0.135 1820 Planarity : 0.003 0.043 2142 Dihedral : 3.494 22.871 1662 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.44 % Allowed : 19.16 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.15 (0.23), residues: 1486 helix: 2.10 (0.20), residues: 716 sheet: -1.20 (0.35), residues: 218 loop : -0.09 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS B 883 PHE 0.010 0.001 PHE A 710 TYR 0.015 0.001 TYR B 555 ARG 0.010 0.000 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 701 ASP cc_start: 0.8146 (t70) cc_final: 0.7918 (t0) REVERT: A 1156 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: B 416 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7623 (p0) REVERT: B 441 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 521 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8436 (ttmm) REVERT: B 701 ASP cc_start: 0.8182 (t70) cc_final: 0.7868 (t0) REVERT: B 878 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8094 (ptpp) REVERT: B 1048 MET cc_start: 0.8635 (mtp) cc_final: 0.8279 (mtt) REVERT: B 1116 LYS cc_start: 0.8356 (pttt) cc_final: 0.8044 (pttt) REVERT: B 1156 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7341 (tt0) outliers start: 32 outliers final: 24 residues processed: 152 average time/residue: 0.2500 time to fit residues: 55.3006 Evaluate side-chains 158 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12446 Z= 0.324 Angle : 0.479 5.217 16816 Z= 0.252 Chirality : 0.040 0.148 1820 Planarity : 0.004 0.046 2142 Dihedral : 3.748 25.319 1662 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.75 % Allowed : 18.93 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.86 (0.23), residues: 1486 helix: 1.86 (0.19), residues: 718 sheet: -1.32 (0.35), residues: 218 loop : -0.25 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1189 HIS 0.005 0.001 HIS B 789 PHE 0.012 0.002 PHE B 710 TYR 0.019 0.001 TYR B 555 ARG 0.009 0.000 ARG B 912 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 441 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8124 (p) REVERT: A 1156 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: B 416 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7604 (p0) REVERT: B 441 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8130 (p) REVERT: B 565 ILE cc_start: 0.9180 (mp) cc_final: 0.8918 (mp) REVERT: B 701 ASP cc_start: 0.8244 (t70) cc_final: 0.7888 (t0) REVERT: B 878 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8127 (ptpp) REVERT: B 1048 MET cc_start: 0.8625 (mtp) cc_final: 0.8283 (mtt) REVERT: B 1116 LYS cc_start: 0.8348 (pttt) cc_final: 0.8028 (pttt) REVERT: B 1156 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7347 (tp30) outliers start: 36 outliers final: 27 residues processed: 154 average time/residue: 0.2300 time to fit residues: 51.8649 Evaluate side-chains 161 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1148 MET Chi-restraints excluded: chain B residue 1156 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.176399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132787 restraints weight = 13027.840| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.31 r_work: 0.3312 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12446 Z= 0.185 Angle : 0.429 5.715 16816 Z= 0.225 Chirality : 0.038 0.139 1820 Planarity : 0.004 0.042 2142 Dihedral : 3.603 24.761 1662 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.44 % Allowed : 19.08 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.02 (0.23), residues: 1486 helix: 1.99 (0.20), residues: 718 sheet: -1.29 (0.35), residues: 218 loop : -0.16 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1189 HIS 0.003 0.001 HIS B 789 PHE 0.010 0.001 PHE A 710 TYR 0.015 0.001 TYR B 555 ARG 0.009 0.000 ARG B 912 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.82 seconds wall clock time: 47 minutes 32.66 seconds (2852.66 seconds total)