Starting phenix.real_space_refine on Wed Jul 30 00:57:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg6_31106/07_2025/7eg6_31106.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg6_31106/07_2025/7eg6_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/cci-nas-00/data/ceres_data/7eg6_31106/07_2025/7eg6_31106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg6_31106/07_2025/7eg6_31106.map" model { file = "/net/cci-nas-00/data/ceres_data/7eg6_31106/07_2025/7eg6_31106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg6_31106/07_2025/7eg6_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.43, per 1000 atoms: 0.70 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: 2.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.91 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: 4.31 Time building geometry restraints manager: 3.46 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: 3.620 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.640 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.150 ------------------------------------------------------------------------------- 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= 0.317 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 Details of bonding type rmsd hydrogen bonds : bond 0.14096 ( 780) hydrogen bonds : angle 4.55852 ( 1955) covalent geometry : bond 0.00716 (12924) covalent geometry : angle 0.73271 (18715) *********************** 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 to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.962 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: 0.3430 time to fit residues: 79.8995 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.082618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055243 restraints weight = 33800.006| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.17 r_work: 0.2634 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 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= 0.200 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 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 780) hydrogen bonds : angle 2.68054 ( 1955) covalent geometry : bond 0.00445 (12924) covalent geometry : angle 0.55203 (18715) *********************** 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 to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8130 (mtt-85) REVERT: A 59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8564 (pm20) REVERT: A 105 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8620 (mt-10) REVERT: B 25 ASN cc_start: 0.8835 (m-40) cc_final: 0.8049 (m110) REVERT: B 59 LYS cc_start: 0.9213 (ttpt) cc_final: 0.9003 (tttt) REVERT: D 34 TYR cc_start: 0.9370 (m-80) cc_final: 0.9090 (m-80) REVERT: D 68 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8481 (mm-30) REVERT: D 73 GLU cc_start: 0.9277 (tp30) cc_final: 0.8932 (tp30) REVERT: D 90 GLU cc_start: 0.9024 (mp0) cc_final: 0.8797 (mp0) REVERT: G 62 ILE cc_start: 0.9516 (mt) cc_final: 0.9307 (tt) REVERT: G 73 ASN cc_start: 0.8977 (m-40) cc_final: 0.8591 (t0) REVERT: H 39 TYR cc_start: 0.8559 (t80) cc_final: 0.8201 (t80) REVERT: H 90 GLU cc_start: 0.9150 (mp0) cc_final: 0.8908 (mp0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.3066 time to fit residues: 66.9999 Evaluate side-chains 152 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 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 B 93 GLN C 38 ASN C 104 GLN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.083204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.055900 restraints weight = 34103.372| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.18 r_work: 0.2648 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1697 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= 0.167 Angle : 0.530 5.778 18715 Z= 0.325 Chirality : 0.033 0.125 2137 Planarity : 0.004 0.041 1362 Dihedral : 30.515 149.234 4058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.31 % Allowed : 9.75 % 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: 2.39 (0.30), residues: 761 helix: 2.43 (0.22), residues: 563 sheet: None (None), residues: 0 loop : -0.98 (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 A 67 TYR 0.012 0.001 TYR F 88 ARG 0.004 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 780) hydrogen bonds : angle 2.54556 ( 1955) covalent geometry : bond 0.00366 (12924) covalent geometry : angle 0.53001 (18715) *********************** 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 168 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8431 (mtp85) cc_final: 0.7932 (mtt-85) REVERT: B 25 ASN cc_start: 0.8835 (m-40) cc_final: 0.8050 (m110) REVERT: D 39 TYR cc_start: 0.8776 (t80) cc_final: 0.8220 (t80) REVERT: D 73 GLU cc_start: 0.9271 (tp30) cc_final: 0.8887 (tp30) REVERT: D 80 TYR cc_start: 0.7956 (m-10) cc_final: 0.7637 (m-80) REVERT: E 90 MET cc_start: 0.8921 (mmp) cc_final: 0.8692 (mmp) REVERT: G 62 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9309 (tt) REVERT: G 73 ASN cc_start: 0.8969 (m-40) cc_final: 0.8621 (t0) REVERT: H 39 TYR cc_start: 0.8518 (t80) cc_final: 0.8126 (t80) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.2975 time to fit residues: 67.0208 Evaluate side-chains 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.055738 restraints weight = 33598.892| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.14 r_work: 0.2653 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1933 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= 0.186 Angle : 0.537 6.659 18715 Z= 0.326 Chirality : 0.033 0.130 2137 Planarity : 0.004 0.039 1362 Dihedral : 30.522 148.038 4058 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.16 % Allowed : 11.32 % Favored : 88.52 % 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: 2.84 (0.30), residues: 761 helix: 2.75 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.032 0.001 TYR F 88 ARG 0.005 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 780) hydrogen bonds : angle 2.51337 ( 1955) covalent geometry : bond 0.00414 (12924) covalent geometry : angle 0.53675 (18715) *********************** 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 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8141 (mtt-85) REVERT: B 25 ASN cc_start: 0.8758 (m-40) cc_final: 0.7964 (m-40) REVERT: D 34 TYR cc_start: 0.9342 (m-80) cc_final: 0.9064 (m-80) REVERT: D 39 TYR cc_start: 0.8741 (t80) cc_final: 0.8222 (t80) REVERT: D 73 GLU cc_start: 0.9306 (tp30) cc_final: 0.8959 (tp30) REVERT: E 90 MET cc_start: 0.8954 (mmp) cc_final: 0.8699 (mmp) REVERT: G 62 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9335 (tt) REVERT: G 73 ASN cc_start: 0.9077 (m-40) cc_final: 0.8764 (t0) REVERT: H 39 TYR cc_start: 0.8510 (t80) cc_final: 0.8021 (t80) REVERT: H 90 GLU cc_start: 0.9050 (mp0) cc_final: 0.8794 (mp0) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.3067 time to fit residues: 65.5209 Evaluate side-chains 151 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.055758 restraints weight = 33728.911| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.16 r_work: 0.2654 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2067 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= 0.188 Angle : 0.536 6.866 18715 Z= 0.325 Chirality : 0.033 0.128 2137 Planarity : 0.004 0.037 1362 Dihedral : 30.521 147.663 4058 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 11.79 % Favored : 87.74 % 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: 2.96 (0.30), residues: 761 helix: 2.84 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -0.78 (0.37), residues: 197 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 0.026 0.002 TYR F 88 ARG 0.005 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 780) hydrogen bonds : angle 2.50629 ( 1955) covalent geometry : bond 0.00418 (12924) covalent geometry : angle 0.53644 (18715) *********************** 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 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8101 (mtt-85) REVERT: B 25 ASN cc_start: 0.8652 (m-40) cc_final: 0.7686 (m110) REVERT: D 56 MET cc_start: 0.9579 (tpt) cc_final: 0.9304 (tpt) REVERT: D 73 GLU cc_start: 0.9307 (tp30) cc_final: 0.8946 (tp30) REVERT: E 90 MET cc_start: 0.8936 (mmp) cc_final: 0.8689 (mmp) REVERT: G 62 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9330 (tt) REVERT: G 73 ASN cc_start: 0.9085 (m-40) cc_final: 0.8769 (t0) REVERT: H 39 TYR cc_start: 0.8498 (t80) cc_final: 0.7991 (t80) REVERT: H 90 GLU cc_start: 0.9120 (mp0) cc_final: 0.8910 (mp0) outliers start: 3 outliers final: 0 residues processed: 156 average time/residue: 0.2983 time to fit residues: 61.9019 Evaluate side-chains 152 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.083542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056026 restraints weight = 33831.659| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.17 r_work: 0.2656 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2137 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= 0.176 Angle : 0.531 7.013 18715 Z= 0.323 Chirality : 0.033 0.125 2137 Planarity : 0.004 0.036 1362 Dihedral : 30.503 147.495 4058 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.31 % Allowed : 12.11 % Favored : 87.58 % 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 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.012 0.001 TYR D 80 ARG 0.005 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 780) hydrogen bonds : angle 2.47965 ( 1955) covalent geometry : bond 0.00390 (12924) covalent geometry : angle 0.53124 (18715) *********************** 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 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8111 (mtt-85) REVERT: A 105 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8612 (mt-10) REVERT: B 25 ASN cc_start: 0.8623 (m-40) cc_final: 0.7643 (m110) REVERT: D 39 TYR cc_start: 0.8801 (t80) cc_final: 0.8255 (t80) REVERT: D 73 GLU cc_start: 0.9308 (tp30) cc_final: 0.8942 (tp30) REVERT: E 90 MET cc_start: 0.8930 (mmp) cc_final: 0.8687 (mmp) REVERT: F 88 TYR cc_start: 0.9027 (m-10) cc_final: 0.8752 (m-10) REVERT: G 62 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9323 (tt) REVERT: G 73 ASN cc_start: 0.9078 (m-40) cc_final: 0.8778 (t0) REVERT: H 39 TYR cc_start: 0.8363 (t80) cc_final: 0.7871 (t80) REVERT: H 90 GLU cc_start: 0.9110 (mp0) cc_final: 0.8910 (mp0) outliers start: 2 outliers final: 1 residues processed: 159 average time/residue: 0.2916 time to fit residues: 62.2170 Evaluate side-chains 159 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER 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 67 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 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 76 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.055902 restraints weight = 33710.893| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.19 r_work: 0.2660 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2171 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= 0.173 Angle : 0.532 7.678 18715 Z= 0.323 Chirality : 0.033 0.125 2137 Planarity : 0.004 0.036 1362 Dihedral : 30.487 147.385 4058 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 13.21 % 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: 2.90 (0.21), 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 0.000 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.014 0.001 TYR D 80 ARG 0.006 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 780) hydrogen bonds : angle 2.46906 ( 1955) covalent geometry : bond 0.00383 (12924) covalent geometry : angle 0.53190 (18715) *********************** 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 162 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8096 (mtt-85) REVERT: B 25 ASN cc_start: 0.8596 (m-40) cc_final: 0.7587 (m110) REVERT: D 73 GLU cc_start: 0.9312 (tp30) cc_final: 0.8949 (tp30) REVERT: E 90 MET cc_start: 0.8931 (mmp) cc_final: 0.8684 (mmp) REVERT: F 88 TYR cc_start: 0.9077 (m-10) cc_final: 0.8811 (m-10) REVERT: G 62 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9314 (tt) REVERT: G 73 ASN cc_start: 0.9079 (m-40) cc_final: 0.8780 (t0) REVERT: H 39 TYR cc_start: 0.8332 (t80) cc_final: 0.7794 (t80) outliers start: 3 outliers final: 1 residues processed: 160 average time/residue: 0.4046 time to fit residues: 87.6385 Evaluate side-chains 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER 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 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.055898 restraints weight = 34206.771| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.18 r_work: 0.2643 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12924 Z= 0.190 Angle : 0.542 7.105 18715 Z= 0.327 Chirality : 0.033 0.125 2137 Planarity : 0.004 0.040 1362 Dihedral : 30.563 146.942 4058 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.68 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: 2.91 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 197 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 0.022 0.001 TYR D 80 ARG 0.006 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 780) hydrogen bonds : angle 2.50334 ( 1955) covalent geometry : bond 0.00425 (12924) covalent geometry : angle 0.54167 (18715) *********************** 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 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8547 (mtp85) cc_final: 0.8163 (mtt-85) REVERT: B 25 ASN cc_start: 0.8619 (m-40) cc_final: 0.7627 (m110) REVERT: D 39 TYR cc_start: 0.8726 (t80) cc_final: 0.8272 (t80) REVERT: D 73 GLU cc_start: 0.9309 (tp30) cc_final: 0.8937 (tp30) REVERT: G 62 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9349 (tt) REVERT: G 73 ASN cc_start: 0.9126 (m-40) cc_final: 0.8829 (t0) REVERT: H 39 TYR cc_start: 0.8475 (t80) cc_final: 0.7976 (t80) REVERT: H 90 GLU cc_start: 0.9070 (mp0) cc_final: 0.8804 (mp0) outliers start: 2 outliers final: 1 residues processed: 155 average time/residue: 0.4635 time to fit residues: 98.1109 Evaluate side-chains 154 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER 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 44 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.084677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057297 restraints weight = 33545.171| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.14 r_work: 0.2694 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12924 Z= 0.156 Angle : 0.528 6.297 18715 Z= 0.320 Chirality : 0.032 0.125 2137 Planarity : 0.004 0.036 1362 Dihedral : 30.289 146.762 4058 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.16 % Allowed : 13.84 % Favored : 86.01 % 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: 3.23 (0.30), residues: 761 helix: 3.01 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.59 (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 0.032 0.001 TYR F 88 ARG 0.007 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 780) hydrogen bonds : angle 2.41239 ( 1955) covalent geometry : bond 0.00340 (12924) covalent geometry : angle 0.52754 (18715) *********************** 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 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8102 (mtt-85) REVERT: B 25 ASN cc_start: 0.8619 (m-40) cc_final: 0.7609 (m110) REVERT: D 39 TYR cc_start: 0.8674 (t80) cc_final: 0.8232 (t80) REVERT: D 73 GLU cc_start: 0.9303 (tp30) cc_final: 0.8918 (tp30) REVERT: F 24 ASP cc_start: 0.7990 (p0) cc_final: 0.7711 (p0) REVERT: G 62 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9205 (tt) REVERT: G 73 ASN cc_start: 0.9050 (m-40) cc_final: 0.8831 (t0) REVERT: H 39 TYR cc_start: 0.8276 (t80) cc_final: 0.7706 (t80) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2896 time to fit residues: 62.0013 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 75 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.083750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056367 restraints weight = 33655.028| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.15 r_work: 0.2663 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12924 Z= 0.181 Angle : 0.540 6.991 18715 Z= 0.327 Chirality : 0.033 0.124 2137 Planarity : 0.004 0.035 1362 Dihedral : 30.419 146.069 4058 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 14.15 % 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: 3.14 (0.30), residues: 761 helix: 2.92 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.62 (0.38), residues: 194 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 0.029 0.001 TYR D 80 ARG 0.009 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 780) hydrogen bonds : angle 2.48698 ( 1955) covalent geometry : bond 0.00402 (12924) covalent geometry : angle 0.54042 (18715) ********************** 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 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8105 (mtt-85) REVERT: B 25 ASN cc_start: 0.8710 (m-40) cc_final: 0.7692 (m110) REVERT: D 39 TYR cc_start: 0.8708 (t80) cc_final: 0.8253 (t80) REVERT: D 73 GLU cc_start: 0.9294 (tp30) cc_final: 0.8930 (tp30) REVERT: F 24 ASP cc_start: 0.8001 (p0) cc_final: 0.7725 (p0) REVERT: G 73 ASN cc_start: 0.9058 (m-40) cc_final: 0.8836 (t0) REVERT: H 39 TYR cc_start: 0.8334 (t80) cc_final: 0.7774 (t80) REVERT: H 90 GLU cc_start: 0.8985 (mp0) cc_final: 0.8766 (mp0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3365 time to fit residues: 70.8146 Evaluate side-chains 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.084082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.056663 restraints weight = 33681.268| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.14 r_work: 0.2672 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12924 Z= 0.160 Angle : 0.537 6.841 18715 Z= 0.325 Chirality : 0.033 0.130 2137 Planarity : 0.004 0.035 1362 Dihedral : 30.409 146.198 4058 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.16 % Allowed : 13.99 % 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: 3.14 (0.30), residues: 761 helix: 2.92 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.61 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.036 0.001 TYR D 80 ARG 0.009 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 780) hydrogen bonds : angle 2.46343 ( 1955) covalent geometry : bond 0.00350 (12924) covalent geometry : angle 0.53679 (18715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6364.37 seconds wall clock time: 112 minutes 40.68 seconds (6760.68 seconds total)