Starting phenix.real_space_refine on Sat Apr 6 09:28:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jni_36448/04_2024/8jni_36448_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 44 5.16 5 Cl 2 4.86 5 C 5212 2.51 5 N 1262 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3879 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 25, 'TRANS': 471} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3879 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 25, 'TRANS': 471} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {' CL': 1, 'PT5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PT5:plan-1': 1, 'PT5:plan-2': 1, 'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {' CL': 1, 'PT5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PT5:plan-1': 1, 'PT5:plan-2': 1, 'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 4.79, per 1000 atoms: 0.61 Number of scatterers: 7842 At special positions: 0 Unit cell: (76.353, 123.971, 77.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 44 16.00 P 6 15.00 O 1316 8.00 N 1262 7.00 C 5212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 855 " - pdb=" SG CYS A 855 " distance=1.99 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 0 sheets defined 69.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'B' and resid 683 through 704 Proline residue: B 694 - end of helix removed outlier: 5.300A pdb=" N LEU B 697 " --> pdb=" O TYR B 693 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER B 698 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 704 " --> pdb=" O PHE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 733 removed outlier: 3.741A pdb=" N ALA B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 718 " --> pdb=" O PHE B 714 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 740 through 757 Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 789 through 810 Processing helix chain 'B' and resid 812 through 818 Processing helix chain 'B' and resid 821 through 849 removed outlier: 3.810A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 923 removed outlier: 3.533A pdb=" N ASN B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 953 removed outlier: 3.559A pdb=" N ARG B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 938 " --> pdb=" O VAL B 934 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 939 " --> pdb=" O ILE B 935 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL B 940 " --> pdb=" O GLY B 936 " (cutoff:3.500A) Proline residue: B 941 - end of helix removed outlier: 3.651A pdb=" N ASP B 951 " --> pdb=" O MET B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1019 removed outlier: 5.667A pdb=" N LEU B 998 " --> pdb=" O MET B 994 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) Proline residue: B1000 - end of helix Processing helix chain 'B' and resid 1032 through 1049 removed outlier: 3.572A pdb=" N LEU B1036 " --> pdb=" O PHE B1032 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B1042 " --> pdb=" O LEU B1038 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B1048 " --> pdb=" O GLY B1044 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE B1049 " --> pdb=" O ILE B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1068 Processing helix chain 'B' and resid 1090 through 1106 removed outlier: 4.209A pdb=" N ILE B1104 " --> pdb=" O VAL B1100 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B1105 " --> pdb=" O GLY B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1130 removed outlier: 3.811A pdb=" N LEU B1130 " --> pdb=" O GLY B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1140 Processing helix chain 'B' and resid 1146 through 1148 No H-bonds generated for 'chain 'B' and resid 1146 through 1148' Processing helix chain 'B' and resid 1153 through 1156 No H-bonds generated for 'chain 'B' and resid 1153 through 1156' Processing helix chain 'B' and resid 1160 through 1182 Processing helix chain 'B' and resid 1187 through 1202 Proline residue: B1190 - end of helix Proline residue: B1198 - end of helix Processing helix chain 'B' and resid 1204 through 1207 No H-bonds generated for 'chain 'B' and resid 1204 through 1207' Processing helix chain 'B' and resid 1210 through 1216 removed outlier: 3.619A pdb=" N CYS B1215 " --> pdb=" O ARG B1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 704 Proline residue: A 694 - end of helix removed outlier: 5.299A pdb=" N LEU A 697 " --> pdb=" O TYR A 693 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 704 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 733 removed outlier: 3.741A pdb=" N ALA A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 740 through 757 Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'A' and resid 789 through 810 Processing helix chain 'A' and resid 812 through 818 Processing helix chain 'A' and resid 821 through 849 removed outlier: 3.810A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 923 removed outlier: 3.532A pdb=" N ASN A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 953 removed outlier: 3.560A pdb=" N ARG A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) Proline residue: A 941 - end of helix removed outlier: 3.651A pdb=" N ASP A 951 " --> pdb=" O MET A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1019 removed outlier: 5.668A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1032 through 1049 removed outlier: 3.572A pdb=" N LEU A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A1048 " --> pdb=" O GLY A1044 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A1049 " --> pdb=" O ILE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1068 Processing helix chain 'A' and resid 1090 through 1106 removed outlier: 4.209A pdb=" N ILE A1104 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A1105 " --> pdb=" O GLY A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1130 removed outlier: 3.810A pdb=" N LEU A1130 " --> pdb=" O GLY A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1153 through 1156 No H-bonds generated for 'chain 'A' and resid 1153 through 1156' Processing helix chain 'A' and resid 1160 through 1182 Processing helix chain 'A' and resid 1187 through 1202 Proline residue: A1190 - end of helix Proline residue: A1198 - end of helix Processing helix chain 'A' and resid 1204 through 1207 No H-bonds generated for 'chain 'A' and resid 1204 through 1207' Processing helix chain 'A' and resid 1210 through 1216 removed outlier: 3.619A pdb=" N CYS A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1254 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: 2.25 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1240 1.32 - 1.44: 2101 1.44 - 1.56: 4611 1.56 - 1.69: 8 1.69 - 1.81: 74 Bond restraints: 8034 Sorted by residual: bond pdb=" C15 PT5 B1402 " pdb=" C16 PT5 B1402 " ideal model delta sigma weight residual 1.360 1.517 -0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C15 PT5 A1301 " pdb=" C16 PT5 A1301 " ideal model delta sigma weight residual 1.360 1.517 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C10 PT5 A1301 " pdb=" O16 PT5 A1301 " ideal model delta sigma weight residual 1.432 1.339 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C10 PT5 B1402 " pdb=" O16 PT5 B1402 " ideal model delta sigma weight residual 1.432 1.340 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O1 PT5 A1301 " pdb=" P1 PT5 A1301 " ideal model delta sigma weight residual 1.650 1.568 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 8029 not shown) Histogram of bond angle deviations from ideal: 99.10 - 107.07: 284 107.07 - 115.04: 4931 115.04 - 123.00: 5388 123.00 - 130.97: 297 130.97 - 138.94: 34 Bond angle restraints: 10934 Sorted by residual: angle pdb=" C15 PT5 B1402 " pdb=" C16 PT5 B1402 " pdb=" C17 PT5 B1402 " ideal model delta sigma weight residual 152.67 113.78 38.89 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C15 PT5 A1301 " pdb=" C16 PT5 A1301 " pdb=" C17 PT5 A1301 " ideal model delta sigma weight residual 152.67 113.80 38.87 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C1 PT5 A1301 " pdb=" O1 PT5 A1301 " pdb=" P1 PT5 A1301 " ideal model delta sigma weight residual 118.43 138.94 -20.51 3.00e+00 1.11e-01 4.67e+01 angle pdb=" C1 PT5 B1402 " pdb=" O1 PT5 B1402 " pdb=" P1 PT5 B1402 " ideal model delta sigma weight residual 118.43 138.90 -20.47 3.00e+00 1.11e-01 4.66e+01 angle pdb=" N VAL B 995 " pdb=" CA VAL B 995 " pdb=" C VAL B 995 " ideal model delta sigma weight residual 112.96 109.09 3.87 1.00e+00 1.00e+00 1.50e+01 ... (remaining 10929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.76: 4599 31.76 - 63.53: 84 63.53 - 95.29: 8 95.29 - 127.05: 0 127.05 - 158.81: 2 Dihedral angle restraints: 4693 sinusoidal: 1831 harmonic: 2862 Sorted by residual: dihedral pdb=" C12 PT5 A1301 " pdb=" C13 PT5 A1301 " pdb=" C14 PT5 A1301 " pdb=" C15 PT5 A1301 " ideal model delta sinusoidal sigma weight residual 21.27 -179.92 -158.81 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C12 PT5 B1402 " pdb=" C13 PT5 B1402 " pdb=" C14 PT5 B1402 " pdb=" C15 PT5 B1402 " ideal model delta sinusoidal sigma weight residual 21.27 -179.93 -158.80 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA LEU A1109 " pdb=" C LEU A1109 " pdb=" N LEU A1110 " pdb=" CA LEU A1110 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 ... (remaining 4690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 1312 1.003 - 2.007: 0 2.007 - 3.010: 0 3.010 - 4.013: 0 4.013 - 5.017: 2 Chirality restraints: 1314 Sorted by residual: chirality pdb=" C5 PT5 B1402 " pdb=" C4 PT5 B1402 " pdb=" C6 PT5 B1402 " pdb=" O5 PT5 B1402 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C5 PT5 A1301 " pdb=" C4 PT5 A1301 " pdb=" C6 PT5 A1301 " pdb=" O5 PT5 A1301 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" CA ILE B 738 " pdb=" N ILE B 738 " pdb=" C ILE B 738 " pdb=" CB ILE B 738 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1311 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 PT5 A1301 " 0.130 2.00e-02 2.50e+03 2.20e-01 4.83e+02 pdb=" C15 PT5 A1301 " -0.282 2.00e-02 2.50e+03 pdb=" C16 PT5 A1301 " 0.282 2.00e-02 2.50e+03 pdb=" C17 PT5 A1301 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 PT5 B1402 " -0.130 2.00e-02 2.50e+03 2.19e-01 4.82e+02 pdb=" C15 PT5 B1402 " 0.282 2.00e-02 2.50e+03 pdb=" C16 PT5 B1402 " -0.282 2.00e-02 2.50e+03 pdb=" C17 PT5 B1402 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 693 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 694 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.028 5.00e-02 4.00e+02 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 878 2.74 - 3.28: 8173 3.28 - 3.82: 13152 3.82 - 4.36: 15619 4.36 - 4.90: 27663 Nonbonded interactions: 65485 Sorted by model distance: nonbonded pdb=" OG SER A 741 " pdb=" OE1 GLU A 742 " model vdw 2.204 2.440 nonbonded pdb=" OG SER B 741 " pdb=" OE1 GLU B 742 " model vdw 2.205 2.440 nonbonded pdb=" O LEU B 730 " pdb=" OG1 THR B 734 " model vdw 2.212 2.440 nonbonded pdb=" O LEU A 730 " pdb=" OG1 THR A 734 " model vdw 2.212 2.440 nonbonded pdb=" O LEU B 907 " pdb=" OG1 THR B 911 " model vdw 2.214 2.440 ... (remaining 65480 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' and resid 673 through 1221) selection = (chain 'B' and resid 673 through 1221) } 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.380 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.800 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.006 0.157 8034 Z= 0.410 Angle : 0.905 38.886 10934 Z= 0.375 Chirality : 0.200 5.017 1314 Planarity : 0.010 0.220 1330 Dihedral : 12.634 158.814 2838 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.93 % Allowed : 5.06 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 982 helix: 0.89 (0.21), residues: 690 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 795 HIS 0.002 0.001 HIS A1064 PHE 0.021 0.001 PHE B1189 TYR 0.014 0.001 TYR B 789 ARG 0.002 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.934 Fit side-chains REVERT: B 930 ARG cc_start: 0.6549 (mtm-85) cc_final: 0.6207 (mtt90) REVERT: A 930 ARG cc_start: 0.6573 (mtm-85) cc_final: 0.6241 (mtt90) outliers start: 16 outliers final: 6 residues processed: 121 average time/residue: 0.2253 time to fit residues: 36.3304 Evaluate side-chains 89 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1189 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1189 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN B1131 ASN A 735 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8034 Z= 0.212 Angle : 0.558 10.139 10934 Z= 0.259 Chirality : 0.040 0.176 1314 Planarity : 0.004 0.048 1330 Dihedral : 10.044 146.589 1106 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.81 % Allowed : 9.52 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 982 helix: 1.06 (0.21), residues: 690 sheet: None (None), residues: 0 loop : 0.25 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 795 HIS 0.002 0.000 HIS B1064 PHE 0.019 0.001 PHE B1189 TYR 0.012 0.001 TYR B 789 ARG 0.002 0.000 ARG A 793 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.915 Fit side-chains REVERT: B 930 ARG cc_start: 0.6430 (mtm-85) cc_final: 0.6120 (mtt90) REVERT: A 930 ARG cc_start: 0.6421 (mtm-85) cc_final: 0.6085 (mtt90) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.1899 time to fit residues: 26.3133 Evaluate side-chains 91 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain B residue 1189 PHE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1189 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 89 optimal weight: 0.0770 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8034 Z= 0.162 Angle : 0.485 9.957 10934 Z= 0.234 Chirality : 0.038 0.125 1314 Planarity : 0.004 0.047 1330 Dihedral : 9.446 138.748 1106 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.29 % Allowed : 10.84 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.28), residues: 982 helix: 1.26 (0.21), residues: 690 sheet: None (None), residues: 0 loop : 0.30 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.002 0.000 HIS A1064 PHE 0.017 0.001 PHE B1189 TYR 0.009 0.001 TYR B 789 ARG 0.005 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.885 Fit side-chains REVERT: B 930 ARG cc_start: 0.6407 (mtm-85) cc_final: 0.6097 (mtt90) REVERT: B 1011 GLU cc_start: 0.7540 (tp30) cc_final: 0.7076 (mt-10) REVERT: A 930 ARG cc_start: 0.6415 (mtm-85) cc_final: 0.6100 (mtt90) REVERT: A 1011 GLU cc_start: 0.7542 (tp30) cc_final: 0.7065 (mt-10) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.1586 time to fit residues: 22.4743 Evaluate side-chains 88 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8034 Z= 0.187 Angle : 0.476 8.867 10934 Z= 0.232 Chirality : 0.038 0.126 1314 Planarity : 0.004 0.049 1330 Dihedral : 8.502 127.204 1102 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.53 % Allowed : 11.81 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 982 helix: 1.29 (0.21), residues: 690 sheet: None (None), residues: 0 loop : 0.31 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.002 0.000 HIS A1064 PHE 0.013 0.001 PHE B1189 TYR 0.009 0.001 TYR B 789 ARG 0.003 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.900 Fit side-chains REVERT: B 930 ARG cc_start: 0.6406 (mtm-85) cc_final: 0.6083 (mtt90) REVERT: B 1011 GLU cc_start: 0.7577 (tp30) cc_final: 0.7067 (mt-10) REVERT: A 930 ARG cc_start: 0.6443 (mtm-85) cc_final: 0.6120 (mtt90) REVERT: A 1011 GLU cc_start: 0.7571 (tp30) cc_final: 0.7071 (mt-10) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.1557 time to fit residues: 23.1032 Evaluate side-chains 91 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8034 Z= 0.249 Angle : 0.505 8.374 10934 Z= 0.247 Chirality : 0.039 0.127 1314 Planarity : 0.004 0.050 1330 Dihedral : 7.860 109.643 1102 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.77 % Allowed : 11.81 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.28), residues: 982 helix: 1.23 (0.21), residues: 690 sheet: None (None), residues: 0 loop : 0.29 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.002 0.000 HIS B1064 PHE 0.015 0.001 PHE B 774 TYR 0.010 0.001 TYR B 789 ARG 0.002 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.865 Fit side-chains REVERT: B 930 ARG cc_start: 0.6443 (mtm-85) cc_final: 0.6149 (mtt90) REVERT: B 1011 GLU cc_start: 0.7625 (tp30) cc_final: 0.7421 (tp30) REVERT: A 930 ARG cc_start: 0.6452 (mtm-85) cc_final: 0.6135 (mtt90) REVERT: A 1011 GLU cc_start: 0.7663 (tp30) cc_final: 0.7457 (tp30) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.1681 time to fit residues: 24.8093 Evaluate side-chains 101 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8034 Z= 0.217 Angle : 0.485 8.677 10934 Z= 0.238 Chirality : 0.038 0.126 1314 Planarity : 0.004 0.050 1330 Dihedral : 7.345 93.966 1102 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.01 % Allowed : 12.05 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.28), residues: 982 helix: 1.26 (0.21), residues: 690 sheet: None (None), residues: 0 loop : 0.34 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.002 0.000 HIS A1064 PHE 0.013 0.001 PHE A 774 TYR 0.010 0.001 TYR B 789 ARG 0.002 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.880 Fit side-chains REVERT: B 930 ARG cc_start: 0.6424 (mtm-85) cc_final: 0.6116 (mtt90) REVERT: B 1011 GLU cc_start: 0.7578 (tp30) cc_final: 0.7055 (mt-10) REVERT: A 930 ARG cc_start: 0.6428 (mtm-85) cc_final: 0.6132 (mtt90) REVERT: A 1011 GLU cc_start: 0.7637 (tp30) cc_final: 0.7116 (mt-10) outliers start: 25 outliers final: 19 residues processed: 99 average time/residue: 0.1698 time to fit residues: 24.6339 Evaluate side-chains 99 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 58 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8034 Z= 0.190 Angle : 0.472 9.060 10934 Z= 0.231 Chirality : 0.038 0.125 1314 Planarity : 0.004 0.050 1330 Dihedral : 6.722 72.914 1102 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.77 % Allowed : 12.53 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.28), residues: 982 helix: 1.33 (0.20), residues: 690 sheet: None (None), residues: 0 loop : 0.38 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.003 0.000 HIS A1064 PHE 0.013 0.001 PHE B 774 TYR 0.008 0.001 TYR B 789 ARG 0.002 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.883 Fit side-chains REVERT: B 930 ARG cc_start: 0.6414 (mtm-85) cc_final: 0.6119 (mtt90) REVERT: B 1011 GLU cc_start: 0.7558 (tp30) cc_final: 0.7045 (mt-10) REVERT: A 930 ARG cc_start: 0.6401 (mtm-85) cc_final: 0.6118 (mtt90) REVERT: A 1011 GLU cc_start: 0.7556 (tp30) cc_final: 0.7047 (mt-10) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.1895 time to fit residues: 27.2079 Evaluate side-chains 99 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8034 Z= 0.196 Angle : 0.486 11.392 10934 Z= 0.234 Chirality : 0.038 0.126 1314 Planarity : 0.004 0.050 1330 Dihedral : 6.297 58.556 1102 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.65 % Allowed : 13.25 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.28), residues: 982 helix: 1.32 (0.20), residues: 690 sheet: None (None), residues: 0 loop : 0.39 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.002 0.000 HIS A1064 PHE 0.012 0.001 PHE B 774 TYR 0.009 0.001 TYR B 789 ARG 0.002 0.000 ARG B 793 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.926 Fit side-chains REVERT: B 930 ARG cc_start: 0.6437 (mtm-85) cc_final: 0.6131 (mtt90) REVERT: B 1011 GLU cc_start: 0.7570 (tp30) cc_final: 0.7077 (mt-10) REVERT: B 1014 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7556 (mt) REVERT: A 930 ARG cc_start: 0.6424 (mtm-85) cc_final: 0.6131 (mtt90) REVERT: A 1011 GLU cc_start: 0.7566 (tp30) cc_final: 0.7050 (mt-10) outliers start: 22 outliers final: 19 residues processed: 97 average time/residue: 0.1696 time to fit residues: 24.3211 Evaluate side-chains 102 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8038 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8034 Z= 0.207 Angle : 0.490 11.233 10934 Z= 0.236 Chirality : 0.038 0.126 1314 Planarity : 0.004 0.050 1330 Dihedral : 6.092 57.148 1102 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.65 % Allowed : 13.37 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.28), residues: 982 helix: 1.33 (0.20), residues: 690 sheet: None (None), residues: 0 loop : 0.39 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.001 0.000 HIS B 850 PHE 0.014 0.001 PHE B 714 TYR 0.009 0.001 TYR B 789 ARG 0.002 0.000 ARG B 793 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.814 Fit side-chains REVERT: B 930 ARG cc_start: 0.6432 (mtm-85) cc_final: 0.6135 (mtt90) REVERT: B 1011 GLU cc_start: 0.7586 (tp30) cc_final: 0.7090 (mt-10) REVERT: B 1014 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7548 (mt) REVERT: A 930 ARG cc_start: 0.6428 (mtm-85) cc_final: 0.6136 (mtt90) REVERT: A 1011 GLU cc_start: 0.7574 (tp30) cc_final: 0.7052 (mt-10) outliers start: 22 outliers final: 21 residues processed: 99 average time/residue: 0.1675 time to fit residues: 24.3440 Evaluate side-chains 106 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8034 Z= 0.183 Angle : 0.481 11.093 10934 Z= 0.232 Chirality : 0.038 0.125 1314 Planarity : 0.004 0.050 1330 Dihedral : 5.958 56.585 1102 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.53 % Allowed : 13.73 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.28), residues: 982 helix: 1.36 (0.20), residues: 690 sheet: None (None), residues: 0 loop : 0.41 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.002 0.000 HIS B1064 PHE 0.012 0.001 PHE B 774 TYR 0.008 0.001 TYR B 789 ARG 0.002 0.000 ARG B 793 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.902 Fit side-chains REVERT: B 930 ARG cc_start: 0.6429 (mtm-85) cc_final: 0.6129 (mtt90) REVERT: B 1011 GLU cc_start: 0.7565 (tp30) cc_final: 0.7083 (mt-10) REVERT: B 1014 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7545 (mt) REVERT: A 930 ARG cc_start: 0.6423 (mtm-85) cc_final: 0.6129 (mtt90) REVERT: A 1011 GLU cc_start: 0.7557 (tp30) cc_final: 0.7050 (mt-10) outliers start: 21 outliers final: 19 residues processed: 97 average time/residue: 0.1681 time to fit residues: 24.0844 Evaluate side-chains 102 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 924 SER Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.150517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123974 restraints weight = 8726.264| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.89 r_work: 0.3270 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8034 Z= 0.157 Angle : 0.469 11.087 10934 Z= 0.226 Chirality : 0.037 0.125 1314 Planarity : 0.004 0.049 1330 Dihedral : 5.782 56.010 1102 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.77 % Allowed : 13.98 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.28), residues: 982 helix: 1.42 (0.21), residues: 690 sheet: None (None), residues: 0 loop : 0.42 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.002 0.000 HIS A1064 PHE 0.012 0.001 PHE B 774 TYR 0.007 0.001 TYR B 789 ARG 0.002 0.000 ARG B 793 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.42 seconds wall clock time: 36 minutes 37.20 seconds (2197.20 seconds total)