Starting phenix.real_space_refine on Thu Sep 26 02:27:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/09_2024/7eg6_31106.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/09_2024/7eg6_31106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/09_2024/7eg6_31106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/09_2024/7eg6_31106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/09_2024/7eg6_31106.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/09_2024/7eg6_31106.cif" } resolution = 3.1 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 12 5.16 5 C 6692 2.51 5 N 2277 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12118 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 159 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 8.04, per 1000 atoms: 0.66 Number of scatterers: 12118 At special positions: 0 Unit cell: (83.7876, 120.31, 129.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 292 15.00 O 2845 8.00 N 2277 7.00 C 6692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 979.6 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.0% alpha, 2.8% beta 144 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.42 Creating SS restraints... Processing helix chain 'M' and resid 665 through 680 removed outlier: 3.794A pdb=" N ASP M 670 " --> pdb=" O ASP M 666 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR M 671 " --> pdb=" O LYS M 667 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG M 676 " --> pdb=" O ARG M 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.585A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.544A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.503A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.655A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.555A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.640A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.561A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.514A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.878A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.603A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.443A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.552A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.841A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.880A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.307A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.972A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.119A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 410 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2035 1.33 - 1.45: 4332 1.45 - 1.56: 5953 1.56 - 1.68: 582 1.68 - 1.80: 22 Bond restraints: 12924 Sorted by residual: bond pdb=" C1' DG I 3 " pdb=" N9 DG I 3 " ideal model delta sigma weight residual 1.460 1.383 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C1' DA I 147 " pdb=" N9 DA I 147 " ideal model delta sigma weight residual 1.460 1.393 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1' DA J 3 " pdb=" N9 DA J 3 " ideal model delta sigma weight residual 1.460 1.400 0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.28e-02 6.10e+03 5.64e+00 bond pdb=" C ILE C 79 " pdb=" N PRO C 80 " ideal model delta sigma weight residual 1.333 1.366 -0.033 1.44e-02 4.82e+03 5.18e+00 ... (remaining 12919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17961 1.66 - 3.33: 707 3.33 - 4.99: 35 4.99 - 6.65: 9 6.65 - 8.32: 3 Bond angle restraints: 18715 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.20 4.90 9.70e-01 1.06e+00 2.55e+01 angle pdb=" N ARG M 676 " pdb=" CA ARG M 676 " pdb=" C ARG M 676 " ideal model delta sigma weight residual 111.36 107.26 4.10 1.09e+00 8.42e-01 1.42e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.64 -5.44 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.09 123.87 -3.78 1.25e+00 6.40e-01 9.16e+00 angle pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sigma weight residual 120.20 124.65 -4.45 1.50e+00 4.44e-01 8.80e+00 ... (remaining 18710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.95: 5346 29.95 - 59.89: 1618 59.89 - 89.84: 49 89.84 - 119.78: 0 119.78 - 149.73: 3 Dihedral angle restraints: 7016 sinusoidal: 4758 harmonic: 2258 Sorted by residual: dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 70.27 149.73 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 79.88 140.12 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 -18.31 -121.69 1 3.50e+01 8.16e-04 1.20e+01 ... (remaining 7013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1496 0.042 - 0.084: 516 0.084 - 0.126: 97 0.126 - 0.168: 27 0.168 - 0.209: 1 Chirality restraints: 2137 Sorted by residual: chirality pdb=" P DG J 95 " pdb=" OP1 DG J 95 " pdb=" OP2 DG J 95 " pdb=" O5' DG J 95 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA VAL G 107 " pdb=" N VAL G 107 " pdb=" C VAL G 107 " pdb=" CB VAL G 107 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 2134 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.77e+00 pdb=" N PRO G 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO E 121 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO C 80 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3622 2.86 - 3.37: 9941 3.37 - 3.88: 24177 3.88 - 4.39: 27558 4.39 - 4.90: 38877 Nonbonded interactions: 104175 Sorted by model distance: nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.348 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.357 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.374 3.040 nonbonded pdb=" O LEU E 92 " pdb=" OG SER E 96 " model vdw 2.374 3.040 ... (remaining 104170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 4.660 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.890 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.007 0.077 12924 Z= 0.418 Angle : 0.733 8.319 18715 Z= 0.452 Chirality : 0.043 0.209 2137 Planarity : 0.006 0.060 1362 Dihedral : 27.432 149.731 5558 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: -1.78 (0.24), residues: 761 helix: -0.88 (0.17), residues: 551 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 18 PHE 0.012 0.002 PHE B 61 TYR 0.011 0.002 TYR C 50 ARG 0.008 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8621 (m-40) cc_final: 0.8087 (m-40) REVERT: B 59 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8676 (ttmm) REVERT: C 92 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8168 (mt-10) REVERT: D 73 GLU cc_start: 0.8984 (tp30) cc_final: 0.8693 (tp30) REVERT: D 80 TYR cc_start: 0.8016 (m-10) cc_final: 0.7648 (m-10) REVERT: D 90 GLU cc_start: 0.8538 (mp0) cc_final: 0.7199 (mp0) REVERT: E 90 MET cc_start: 0.8641 (mmm) cc_final: 0.8441 (mmp) REVERT: F 31 LYS cc_start: 0.9081 (tttt) cc_final: 0.8843 (tttp) REVERT: F 88 TYR cc_start: 0.9078 (m-10) cc_final: 0.8818 (m-80) REVERT: G 73 ASN cc_start: 0.8943 (m110) cc_final: 0.8639 (t0) REVERT: H 39 TYR cc_start: 0.8196 (t80) cc_final: 0.7766 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3406 time to fit residues: 79.1041 Evaluate side-chains 155 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 55 GLN A 68 GLN A 76 GLN B 93 GLN C 104 GLN D 79 HIS D 92 GLN E 68 GLN E 125 GLN F 25 ASN F 93 GLN G 73 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12924 Z= 0.248 Angle : 0.552 5.868 18715 Z= 0.337 Chirality : 0.034 0.133 2137 Planarity : 0.005 0.047 1362 Dihedral : 30.586 149.501 4058 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % 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: 761 helix: 1.62 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR C 57 ARG 0.004 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7936 (mtt-85) REVERT: A 105 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 25 ASN cc_start: 0.8729 (m-40) cc_final: 0.8001 (m110) REVERT: B 59 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8837 (tttt) REVERT: D 34 TYR cc_start: 0.9276 (m-80) cc_final: 0.9001 (m-80) REVERT: D 73 GLU cc_start: 0.8991 (tp30) cc_final: 0.8617 (tp30) REVERT: D 90 GLU cc_start: 0.8696 (mp0) cc_final: 0.8415 (mp0) REVERT: F 31 LYS cc_start: 0.8925 (tttt) cc_final: 0.8720 (tttp) REVERT: F 88 TYR cc_start: 0.9072 (m-10) cc_final: 0.8862 (m-80) REVERT: G 62 ILE cc_start: 0.9432 (mt) cc_final: 0.9223 (tt) REVERT: G 73 ASN cc_start: 0.8908 (m-40) cc_final: 0.8551 (t0) REVERT: H 39 TYR cc_start: 0.7910 (t80) cc_final: 0.7481 (t80) REVERT: H 65 ASP cc_start: 0.9024 (t0) cc_final: 0.8824 (t0) REVERT: H 90 GLU cc_start: 0.8916 (mp0) cc_final: 0.8628 (mp0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.3283 time to fit residues: 71.9953 Evaluate side-chains 153 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 93 GLN C 38 ASN C 104 GLN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.248 Angle : 0.545 6.197 18715 Z= 0.332 Chirality : 0.034 0.126 2137 Planarity : 0.004 0.041 1362 Dihedral : 30.586 149.328 4058 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.16 % Allowed : 9.91 % Favored : 89.94 % 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: 2.38 (0.30), residues: 761 helix: 2.43 (0.22), residues: 563 sheet: None (None), residues: 0 loop : -1.05 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.012 0.001 TYR H 118 ARG 0.005 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7876 (mtt-85) REVERT: B 25 ASN cc_start: 0.8731 (m-40) cc_final: 0.8082 (m-40) REVERT: D 39 TYR cc_start: 0.8095 (t80) cc_final: 0.7408 (t80) REVERT: D 56 MET cc_start: 0.9256 (tpt) cc_final: 0.9027 (tpt) REVERT: D 73 GLU cc_start: 0.8990 (tp30) cc_final: 0.8598 (tp30) REVERT: D 80 TYR cc_start: 0.7743 (m-10) cc_final: 0.7464 (m-80) REVERT: D 90 GLU cc_start: 0.8659 (mp0) cc_final: 0.8389 (mp0) REVERT: E 90 MET cc_start: 0.8406 (mmp) cc_final: 0.8168 (mmp) REVERT: F 31 LYS cc_start: 0.8945 (tttt) cc_final: 0.8728 (tttp) REVERT: F 84 MET cc_start: 0.8790 (tpt) cc_final: 0.8520 (tpt) REVERT: G 62 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9235 (tt) REVERT: G 73 ASN cc_start: 0.8935 (m-40) cc_final: 0.8598 (t0) REVERT: H 39 TYR cc_start: 0.7896 (t80) cc_final: 0.7455 (t80) REVERT: H 90 GLU cc_start: 0.8917 (mp0) cc_final: 0.8682 (mp0) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.3170 time to fit residues: 66.7072 Evaluate side-chains 154 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 38 ASN C 104 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12924 Z= 0.282 Angle : 0.553 6.920 18715 Z= 0.335 Chirality : 0.035 0.124 2137 Planarity : 0.004 0.037 1362 Dihedral : 30.652 148.519 4058 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.47 % Allowed : 10.53 % Favored : 88.99 % 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: 2.74 (0.30), residues: 761 helix: 2.71 (0.22), residues: 563 sheet: None (None), residues: 0 loop : -0.97 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.012 0.001 TYR H 118 ARG 0.005 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7862 (mtt-85) REVERT: A 105 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 25 ASN cc_start: 0.8747 (m-40) cc_final: 0.7824 (m110) REVERT: D 34 TYR cc_start: 0.9238 (m-80) cc_final: 0.9004 (m-80) REVERT: D 73 GLU cc_start: 0.8995 (tp30) cc_final: 0.8627 (tp30) REVERT: D 90 GLU cc_start: 0.8645 (mp0) cc_final: 0.8402 (mp0) REVERT: E 73 GLU cc_start: 0.8243 (tt0) cc_final: 0.8033 (tt0) REVERT: E 90 MET cc_start: 0.8448 (mmp) cc_final: 0.8189 (mmp) REVERT: F 31 LYS cc_start: 0.8960 (tttt) cc_final: 0.8735 (tttp) REVERT: F 88 TYR cc_start: 0.8953 (m-80) cc_final: 0.8706 (m-10) REVERT: G 62 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9259 (tt) REVERT: G 73 ASN cc_start: 0.8970 (m-40) cc_final: 0.8640 (t0) REVERT: H 39 TYR cc_start: 0.7938 (t80) cc_final: 0.7455 (t80) REVERT: H 90 GLU cc_start: 0.8934 (mp0) cc_final: 0.8707 (mp0) outliers start: 3 outliers final: 0 residues processed: 160 average time/residue: 0.3161 time to fit residues: 67.1266 Evaluate side-chains 152 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.247 Angle : 0.543 6.862 18715 Z= 0.330 Chirality : 0.034 0.126 2137 Planarity : 0.004 0.036 1362 Dihedral : 30.633 148.283 4058 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.47 % Allowed : 11.16 % Favored : 88.36 % 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: 2.90 (0.30), residues: 761 helix: 2.80 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -0.85 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.011 0.001 TYR H 118 ARG 0.009 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7881 (mtt-85) REVERT: A 105 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 25 ASN cc_start: 0.8719 (m-40) cc_final: 0.7790 (m110) REVERT: D 56 MET cc_start: 0.9308 (tpt) cc_final: 0.8961 (tpt) REVERT: D 73 GLU cc_start: 0.9027 (tp30) cc_final: 0.8649 (tp30) REVERT: D 90 GLU cc_start: 0.8636 (mp0) cc_final: 0.8351 (mp0) REVERT: E 90 MET cc_start: 0.8436 (mmp) cc_final: 0.8194 (mmp) REVERT: F 31 LYS cc_start: 0.8946 (tttt) cc_final: 0.8722 (tttp) REVERT: G 62 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9258 (tt) REVERT: G 73 ASN cc_start: 0.8973 (m-40) cc_final: 0.8649 (t0) REVERT: G 90 ASP cc_start: 0.8836 (t0) cc_final: 0.8474 (t70) REVERT: H 39 TYR cc_start: 0.7742 (t80) cc_final: 0.7194 (t80) REVERT: H 90 GLU cc_start: 0.8922 (mp0) cc_final: 0.8680 (mp0) outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.3035 time to fit residues: 63.9398 Evaluate side-chains 153 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12924 Z= 0.267 Angle : 0.549 6.944 18715 Z= 0.332 Chirality : 0.034 0.126 2137 Planarity : 0.004 0.035 1362 Dihedral : 30.673 147.972 4058 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.16 % Allowed : 11.16 % Favored : 88.68 % 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: 2.90 (0.30), residues: 761 helix: 2.79 (0.22), residues: 567 sheet: None (None), residues: 0 loop : -0.86 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.037 0.002 TYR F 88 ARG 0.009 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8332 (mtp85) cc_final: 0.7810 (mtt-85) REVERT: A 105 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 25 ASN cc_start: 0.8693 (m-40) cc_final: 0.7716 (m110) REVERT: D 56 MET cc_start: 0.9300 (tpt) cc_final: 0.8982 (tpt) REVERT: D 73 GLU cc_start: 0.9028 (tp30) cc_final: 0.8664 (tp30) REVERT: D 90 GLU cc_start: 0.8631 (mp0) cc_final: 0.8411 (mp0) REVERT: E 90 MET cc_start: 0.8453 (mmp) cc_final: 0.8205 (mmp) REVERT: F 31 LYS cc_start: 0.8953 (tttt) cc_final: 0.8726 (tttp) REVERT: G 62 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9231 (tt) REVERT: G 73 ASN cc_start: 0.9003 (m-40) cc_final: 0.8679 (t0) REVERT: H 39 TYR cc_start: 0.7769 (t80) cc_final: 0.7225 (t80) REVERT: H 65 ASP cc_start: 0.9075 (t0) cc_final: 0.8778 (t0) REVERT: H 90 GLU cc_start: 0.8919 (mp0) cc_final: 0.8706 (mp0) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.3152 time to fit residues: 66.0345 Evaluate side-chains 156 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12924 Z= 0.208 Angle : 0.533 6.546 18715 Z= 0.325 Chirality : 0.033 0.125 2137 Planarity : 0.004 0.035 1362 Dihedral : 30.594 147.701 4058 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.31 % Allowed : 12.89 % Favored : 86.79 % 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: 3.04 (0.30), residues: 761 helix: 2.89 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -0.73 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 79 PHE 0.009 0.001 PHE B 61 TYR 0.029 0.002 TYR F 88 ARG 0.008 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7869 (mtt-85) REVERT: A 105 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 25 ASN cc_start: 0.8677 (m-40) cc_final: 0.7680 (m110) REVERT: D 56 MET cc_start: 0.9311 (tpt) cc_final: 0.8939 (tpt) REVERT: D 73 GLU cc_start: 0.9004 (tp30) cc_final: 0.8618 (tp30) REVERT: D 90 GLU cc_start: 0.8619 (mp0) cc_final: 0.8393 (mp0) REVERT: E 90 MET cc_start: 0.8427 (mmp) cc_final: 0.8180 (mmp) REVERT: F 24 ASP cc_start: 0.7323 (p0) cc_final: 0.7085 (p0) REVERT: F 31 LYS cc_start: 0.8935 (tttt) cc_final: 0.8698 (tttp) REVERT: G 62 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9191 (tt) REVERT: G 73 ASN cc_start: 0.9040 (m-40) cc_final: 0.8718 (t0) REVERT: H 39 TYR cc_start: 0.7650 (t80) cc_final: 0.7131 (t80) REVERT: H 65 ASP cc_start: 0.9057 (t0) cc_final: 0.8801 (t0) REVERT: H 76 ARG cc_start: 0.8597 (ttm170) cc_final: 0.8382 (ttt90) REVERT: H 90 GLU cc_start: 0.8883 (mp0) cc_final: 0.8663 (mp0) outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.3091 time to fit residues: 66.2413 Evaluate side-chains 159 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12924 Z= 0.246 Angle : 0.544 6.694 18715 Z= 0.330 Chirality : 0.033 0.129 2137 Planarity : 0.004 0.035 1362 Dihedral : 30.620 147.399 4058 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.31 % Allowed : 13.36 % Favored : 86.32 % 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: 3.06 (0.30), residues: 761 helix: 2.89 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.031 0.002 TYR F 88 ARG 0.009 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7862 (mtt-85) REVERT: A 105 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 25 ASN cc_start: 0.8687 (m-40) cc_final: 0.7719 (m110) REVERT: D 39 TYR cc_start: 0.8064 (t80) cc_final: 0.7423 (t80) REVERT: D 56 MET cc_start: 0.9318 (tpt) cc_final: 0.8974 (tpt) REVERT: D 73 GLU cc_start: 0.9008 (tp30) cc_final: 0.8647 (tp30) REVERT: D 90 GLU cc_start: 0.8636 (mp0) cc_final: 0.8338 (mp0) REVERT: F 24 ASP cc_start: 0.7297 (p0) cc_final: 0.7082 (p0) REVERT: F 31 LYS cc_start: 0.8945 (tttt) cc_final: 0.8719 (tttp) REVERT: G 62 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9183 (tt) REVERT: G 73 ASN cc_start: 0.9039 (m-40) cc_final: 0.8728 (t0) REVERT: H 39 TYR cc_start: 0.7682 (t80) cc_final: 0.7119 (t80) REVERT: H 65 ASP cc_start: 0.9078 (t0) cc_final: 0.8800 (t0) REVERT: H 90 GLU cc_start: 0.8911 (mp0) cc_final: 0.8679 (mp0) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.3037 time to fit residues: 62.9612 Evaluate side-chains 159 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.0020 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.202 Angle : 0.539 6.723 18715 Z= 0.327 Chirality : 0.033 0.124 2137 Planarity : 0.004 0.038 1362 Dihedral : 30.518 147.133 4058 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.16 % Allowed : 13.21 % Favored : 86.64 % 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: 3.14 (0.30), residues: 761 helix: 2.94 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -0.62 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 79 PHE 0.009 0.001 PHE B 61 TYR 0.018 0.001 TYR B 88 ARG 0.009 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7889 (mtt-85) REVERT: A 105 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8081 (mt-10) REVERT: B 25 ASN cc_start: 0.8665 (m-40) cc_final: 0.7671 (m110) REVERT: D 56 MET cc_start: 0.9322 (tpt) cc_final: 0.8906 (tpt) REVERT: D 73 GLU cc_start: 0.9008 (tp30) cc_final: 0.8630 (tp30) REVERT: D 90 GLU cc_start: 0.8620 (mp0) cc_final: 0.8390 (mp0) REVERT: F 31 LYS cc_start: 0.8929 (tttt) cc_final: 0.8691 (tttp) REVERT: G 62 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9140 (tt) REVERT: G 73 ASN cc_start: 0.9026 (m-40) cc_final: 0.8742 (t0) REVERT: G 94 ASN cc_start: 0.9170 (t0) cc_final: 0.8947 (t0) REVERT: H 39 TYR cc_start: 0.7607 (t80) cc_final: 0.7068 (t80) REVERT: H 65 ASP cc_start: 0.9053 (t0) cc_final: 0.8799 (t0) REVERT: H 90 GLU cc_start: 0.8914 (mp0) cc_final: 0.8695 (mp0) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.3180 time to fit residues: 69.5759 Evaluate side-chains 159 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN D 79 HIS F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.217 Angle : 0.545 6.283 18715 Z= 0.330 Chirality : 0.033 0.127 2137 Planarity : 0.004 0.036 1362 Dihedral : 30.470 146.719 4058 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.31 % Allowed : 13.36 % Favored : 86.32 % 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: 3.10 (0.30), residues: 761 helix: 2.89 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.63 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 79 PHE 0.009 0.001 PHE B 61 TYR 0.024 0.002 TYR B 88 ARG 0.009 0.000 ARG D 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7902 (mtt-85) REVERT: B 25 ASN cc_start: 0.8625 (m-40) cc_final: 0.7621 (m110) REVERT: D 39 TYR cc_start: 0.8038 (t80) cc_final: 0.7408 (t80) REVERT: D 56 MET cc_start: 0.9323 (tpt) cc_final: 0.8912 (tpt) REVERT: D 73 GLU cc_start: 0.8980 (tp30) cc_final: 0.8604 (tp30) REVERT: D 90 GLU cc_start: 0.8611 (mp0) cc_final: 0.8328 (mp0) REVERT: F 31 LYS cc_start: 0.8928 (tttt) cc_final: 0.8705 (tttp) REVERT: F 88 TYR cc_start: 0.8696 (m-10) cc_final: 0.8422 (m-10) REVERT: G 62 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9146 (tt) REVERT: G 73 ASN cc_start: 0.9011 (m-40) cc_final: 0.8749 (t0) REVERT: H 39 TYR cc_start: 0.7629 (t80) cc_final: 0.7051 (t80) REVERT: H 65 ASP cc_start: 0.9065 (t0) cc_final: 0.8805 (t0) REVERT: H 90 GLU cc_start: 0.8915 (mp0) cc_final: 0.8687 (mp0) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.3289 time to fit residues: 68.5583 Evaluate side-chains 156 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.0470 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.084311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056904 restraints weight = 33559.813| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.14 r_work: 0.2677 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.210 Angle : 0.543 6.165 18715 Z= 0.328 Chirality : 0.032 0.125 2137 Planarity : 0.004 0.037 1362 Dihedral : 30.404 146.474 4058 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.31 % Allowed : 13.84 % Favored : 85.85 % 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: 3.28 (0.30), residues: 761 helix: 3.04 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.56 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 79 PHE 0.009 0.001 PHE B 61 TYR 0.025 0.001 TYR D 80 ARG 0.009 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.29 seconds wall clock time: 46 minutes 49.71 seconds (2809.71 seconds total)