Starting phenix.real_space_refine on Fri Mar 15 14:18:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/03_2024/8euj_28614_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/03_2024/8euj_28614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/03_2024/8euj_28614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/03_2024/8euj_28614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/03_2024/8euj_28614_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/03_2024/8euj_28614_neut.pdb" } resolution = 3.36 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= 0.004 sd= 0.104 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 6591 2.51 5 N 2205 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 32": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M ASP 81": "OD1" <-> "OD2" Residue "M TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 105": "OE1" <-> "OE2" Residue "O ASP 24": "OD1" <-> "OD2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "a ASP 90": "OD1" <-> "OD2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "b PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 73": "OE1" <-> "OE2" Residue "b GLU 110": "OE1" <-> "OE2" Residue "f TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 59": "OE1" <-> "OE2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "h TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 63": "OE1" <-> "OE2" Residue "h TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 56": "OE1" <-> "OE2" Residue "k GLU 61": "OE1" <-> "OE2" Residue "k GLU 64": "OE1" <-> "OE2" Residue "k ASP 72": "OD1" <-> "OD2" Residue "k ASP 90": "OD1" <-> "OD2" Residue "k GLU 91": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11913 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 765 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "b" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "f" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 782 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU O 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU O 22 " occ=0.00 residue: pdb=" N ARG O 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG O 23 " occ=0.00 Time building chain proxies: 6.78, per 1000 atoms: 0.57 Number of scatterers: 11913 At special positions: 0 Unit cell: (116.065, 120.24, 104.375, 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 2813 8.00 N 2205 7.00 C 6591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 73.0% alpha, 1.6% beta 147 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 5.89 Creating SS restraints... Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.503A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.765A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.520A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.545A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.555A pdb=" N ALA M 114 " --> pdb=" O CYS M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.779A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 29 removed outlier: 4.088A pdb=" N ILE O 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 41 Processing helix chain 'O' and resid 50 through 76 removed outlier: 4.044A pdb=" N ASP O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 93 removed outlier: 3.745A pdb=" N VAL O 86 " --> pdb=" O THR O 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 22 Processing helix chain 'a' and resid 26 through 37 Processing helix chain 'a' and resid 45 through 72 removed outlier: 4.141A pdb=" N VAL a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 89 removed outlier: 3.666A pdb=" N ASN a 89 " --> pdb=" O LEU a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 97 Processing helix chain 'b' and resid 34 through 46 removed outlier: 4.186A pdb=" N VAL b 38 " --> pdb=" O TYR b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 80 Processing helix chain 'b' and resid 87 through 99 removed outlier: 3.759A pdb=" N LEU b 98 " --> pdb=" O ALA b 94 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU b 99 " --> pdb=" O VAL b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 121 removed outlier: 3.884A pdb=" N ALA b 121 " --> pdb=" O LYS b 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 57 Processing helix chain 'f' and resid 63 through 79 removed outlier: 3.955A pdb=" N PHE f 67 " --> pdb=" O ARG f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 114 Processing helix chain 'f' and resid 121 through 131 Processing helix chain 'h' and resid 24 through 29 removed outlier: 3.529A pdb=" N GLN h 27 " --> pdb=" O ASP h 24 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE h 29 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 42 Processing helix chain 'h' and resid 49 through 76 removed outlier: 3.612A pdb=" N ALA h 76 " --> pdb=" O TYR h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 94 removed outlier: 3.823A pdb=" N VAL h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 22 removed outlier: 3.776A pdb=" N ARG k 20 " --> pdb=" O THR k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 36 removed outlier: 3.995A pdb=" N VAL k 30 " --> pdb=" O PRO k 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 74 removed outlier: 4.404A pdb=" N VAL k 49 " --> pdb=" O ALA k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 88 Processing helix chain 'k' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'H' and resid 50 through 51 removed outlier: 7.857A pdb=" N GLY H 50 " --> pdb=" O ILE k 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG M 83 " --> pdb=" O VAL O 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 96 through 97 removed outlier: 6.869A pdb=" N THR O 96 " --> pdb=" O THR k 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'f' and resid 83 through 84 removed outlier: 7.148A pdb=" N ARG f 83 " --> pdb=" O VAL h 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 390 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2637 1.34 - 1.46: 4499 1.46 - 1.58: 4978 1.58 - 1.71: 585 1.71 - 1.83: 22 Bond restraints: 12721 Sorted by residual: bond pdb=" C ILE a 79 " pdb=" N PRO a 80 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.08e-02 8.57e+03 9.40e+00 bond pdb=" CB PRO a 109 " pdb=" CG PRO a 109 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.96e+00 bond pdb=" CB ASN k 73 " pdb=" CG ASN k 73 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.15e+00 bond pdb=" CB ASN H 60 " pdb=" CG ASN H 60 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.91e+00 bond pdb=" CB ASN a 38 " pdb=" CG ASN a 38 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.76e+00 ... (remaining 12716 not shown) Histogram of bond angle deviations from ideal: 97.34 - 105.81: 1661 105.81 - 114.29: 7315 114.29 - 122.76: 7622 122.76 - 131.24: 1755 131.24 - 139.71: 95 Bond angle restraints: 18448 Sorted by residual: angle pdb=" CA PRO a 109 " pdb=" N PRO a 109 " pdb=" CD PRO a 109 " ideal model delta sigma weight residual 112.00 99.08 12.92 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA LEU f 65 " pdb=" CB LEU f 65 " pdb=" CG LEU f 65 " ideal model delta sigma weight residual 116.30 139.71 -23.41 3.50e+00 8.16e-02 4.47e+01 angle pdb=" CA PRO f 43 " pdb=" N PRO f 43 " pdb=" CD PRO f 43 " ideal model delta sigma weight residual 112.00 103.70 8.30 1.40e+00 5.10e-01 3.51e+01 angle pdb=" CA LYS M 64 " pdb=" CB LYS M 64 " pdb=" CG LYS M 64 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.51e+01 angle pdb=" CA ARG b 89 " pdb=" CB ARG b 89 " pdb=" CG ARG b 89 " ideal model delta sigma weight residual 114.10 125.01 -10.91 2.00e+00 2.50e-01 2.98e+01 ... (remaining 18443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3951 18.00 - 36.00: 1366 36.00 - 54.00: 1251 54.00 - 72.00: 355 72.00 - 90.00: 52 Dihedral angle restraints: 6975 sinusoidal: 4809 harmonic: 2166 Sorted by residual: dihedral pdb=" CA ILE O 50 " pdb=" C ILE O 50 " pdb=" N TYR O 51 " pdb=" CA TYR O 51 " ideal model delta harmonic sigma weight residual 180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU b 97 " pdb=" C LEU b 97 " pdb=" N LEU b 98 " pdb=" CA LEU b 98 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU a 108 " pdb=" C LEU a 108 " pdb=" N PRO a 109 " pdb=" CA PRO a 109 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1866 0.083 - 0.167: 213 0.167 - 0.250: 17 0.250 - 0.334: 4 0.334 - 0.417: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CB VAL H 108 " pdb=" CA VAL H 108 " pdb=" CG1 VAL H 108 " pdb=" CG2 VAL H 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB ILE H 58 " pdb=" CA ILE H 58 " pdb=" CG1 ILE H 58 " pdb=" CG2 ILE H 58 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CB VAL H 41 " pdb=" CA VAL H 41 " pdb=" CG1 VAL H 41 " pdb=" CG2 VAL H 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2101 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a 108 " -0.106 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO a 109 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO a 109 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO a 109 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG f 42 " 0.069 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO f 43 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO f 43 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO f 43 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR h 88 " 0.026 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR h 88 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR h 88 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR h 88 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR h 88 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR h 88 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR h 88 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR h 88 " -0.002 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1827 2.77 - 3.30: 10431 3.30 - 3.83: 25130 3.83 - 4.37: 27389 4.37 - 4.90: 37898 Nonbonded interactions: 102675 Sorted by model distance: nonbonded pdb=" O LEU a 55 " pdb=" OG1 THR a 59 " model vdw 2.233 2.440 nonbonded pdb=" OD2 ASP b 65 " pdb=" OH TYR h 98 " model vdw 2.259 2.440 nonbonded pdb=" OP1 DT J 18 " pdb=" NZ LYS M 64 " model vdw 2.267 2.520 nonbonded pdb=" O TYR a 39 " pdb=" OG SER b 75 " model vdw 2.291 2.440 nonbonded pdb=" OD2 ASP H 65 " pdb=" OH TYR O 98 " model vdw 2.294 2.440 ... (remaining 102670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'H' and resid 30 through 121) selection = (chain 'b' and (resid 30 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 121)) } ncs_group { reference = (chain 'I' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'J' and (resid -73 through -1 or resid 1 through 73)) } ncs_group { reference = (chain 'M' and (resid 41 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 135)) selection = (chain 'f' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 133 or (resid 134 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'O' and (resid 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 102)) selection = chain 'h' } ncs_group { reference = (chain 'a' and resid 15 through 118) selection = chain 'k' } 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=0.00 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: 11.390 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: 0.000 Extract box with map and model: 19.090 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 41.700 Find NCS groups from input model: 0.620 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 12721 Z= 0.349 Angle : 1.221 23.411 18448 Z= 0.645 Chirality : 0.057 0.417 2104 Planarity : 0.011 0.150 1319 Dihedral : 30.772 89.997 5577 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 40.55 % Favored : 59.45 % 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: -2.60 (0.27), residues: 730 helix: -1.65 (0.19), residues: 517 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS O 75 PHE 0.056 0.004 PHE O 61 TYR 0.065 0.005 TYR h 88 ARG 0.024 0.002 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7442 (mm-30) REVERT: a 112 GLN cc_start: 0.6722 (tp-100) cc_final: 0.6424 (tm-30) REVERT: b 73 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7758 (mm-30) REVERT: b 76 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8527 (ttm110) REVERT: f 90 MET cc_start: 0.8427 (mmm) cc_final: 0.8214 (mmm) REVERT: k 35 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8339 (mpp80) REVERT: k 71 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8224 (mtt90) REVERT: k 91 GLU cc_start: 0.8103 (pp20) cc_final: 0.7599 (pp20) REVERT: k 92 GLU cc_start: 0.7888 (pm20) cc_final: 0.7657 (pm20) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2985 time to fit residues: 107.5095 Evaluate side-chains 258 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.0000 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 125 GLN O 93 GLN ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 HIS k 82 HIS k 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12721 Z= 0.211 Angle : 0.722 17.457 18448 Z= 0.412 Chirality : 0.037 0.213 2104 Planarity : 0.006 0.079 1319 Dihedral : 32.282 89.796 4127 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.86 % Allowed : 34.20 % Favored : 59.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.29), residues: 730 helix: -0.17 (0.21), residues: 523 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS O 75 PHE 0.011 0.001 PHE H 67 TYR 0.036 0.002 TYR O 88 ARG 0.013 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 131 ARG cc_start: 0.7858 (ptm160) cc_final: 0.7325 (ptp-170) REVERT: a 33 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9066 (mm) REVERT: b 76 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8587 (ttm110) REVERT: h 27 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7584 (tp-100) REVERT: k 35 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8347 (mpp80) REVERT: k 91 GLU cc_start: 0.8203 (pp20) cc_final: 0.7785 (pp20) outliers start: 36 outliers final: 26 residues processed: 268 average time/residue: 0.3113 time to fit residues: 110.2422 Evaluate side-chains 257 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 228 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 0.0000 chunk 97 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 93 GLN ** a 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN b 79 HIS k 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12721 Z= 0.203 Angle : 0.705 15.459 18448 Z= 0.402 Chirality : 0.037 0.188 2104 Planarity : 0.005 0.064 1319 Dihedral : 32.110 87.076 4127 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.68 % Allowed : 33.22 % Favored : 60.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.30), residues: 730 helix: 0.51 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.45 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS b 79 PHE 0.013 0.001 PHE b 62 TYR 0.042 0.002 TYR O 88 ARG 0.009 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 250 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 40 LYS cc_start: 0.8979 (pttm) cc_final: 0.8544 (ptpp) REVERT: a 33 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9020 (mm) REVERT: a 65 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8129 (mm) REVERT: a 95 LYS cc_start: 0.9297 (ttmm) cc_final: 0.8915 (mtpp) REVERT: b 64 ASN cc_start: 0.8786 (m-40) cc_final: 0.8458 (m110) REVERT: b 76 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8509 (ttm110) REVERT: b 113 LYS cc_start: 0.7717 (pptt) cc_final: 0.7476 (pptt) REVERT: h 27 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7590 (tp-100) REVERT: h 35 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8118 (mmm-85) REVERT: k 35 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8344 (mpp80) REVERT: k 91 GLU cc_start: 0.8306 (pp20) cc_final: 0.7804 (pp20) outliers start: 41 outliers final: 25 residues processed: 269 average time/residue: 0.2860 time to fit residues: 102.5251 Evaluate side-chains 262 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.0020 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN k 24 GLN k 38 ASN k 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12721 Z= 0.199 Angle : 0.687 14.294 18448 Z= 0.394 Chirality : 0.037 0.214 2104 Planarity : 0.005 0.055 1319 Dihedral : 31.930 88.090 4127 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 7.49 % Allowed : 30.78 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.30), residues: 730 helix: 0.86 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS O 75 PHE 0.019 0.002 PHE O 61 TYR 0.046 0.002 TYR O 88 ARG 0.010 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8836 (tptt) cc_final: 0.8565 (tppt) REVERT: a 33 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9025 (mm) REVERT: a 42 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7622 (ttp80) REVERT: a 65 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8190 (mm) REVERT: a 95 LYS cc_start: 0.9304 (ttmm) cc_final: 0.8939 (mtpp) REVERT: b 73 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7978 (mm-30) REVERT: b 76 ARG cc_start: 0.8917 (ttm110) cc_final: 0.8559 (ttm110) REVERT: b 113 LYS cc_start: 0.7707 (pptt) cc_final: 0.7471 (pttp) REVERT: f 90 MET cc_start: 0.8412 (mmm) cc_final: 0.8185 (mmm) REVERT: h 27 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7540 (tp-100) REVERT: h 66 ILE cc_start: 0.8984 (pt) cc_final: 0.8581 (mt) REVERT: k 23 LEU cc_start: 0.7323 (mt) cc_final: 0.6982 (mp) REVERT: k 24 GLN cc_start: 0.7078 (tp40) cc_final: 0.6651 (tt0) REVERT: k 35 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8335 (mpp80) REVERT: k 91 GLU cc_start: 0.8369 (pp20) cc_final: 0.7854 (pp20) outliers start: 46 outliers final: 33 residues processed: 275 average time/residue: 0.2875 time to fit residues: 105.0583 Evaluate side-chains 274 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 60 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 0.2980 chunk 81 optimal weight: 0.0470 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN ** a 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 HIS ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12721 Z= 0.186 Angle : 0.692 13.097 18448 Z= 0.392 Chirality : 0.036 0.179 2104 Planarity : 0.005 0.057 1319 Dihedral : 31.809 88.170 4127 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.72 % Allowed : 34.85 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 730 helix: 0.91 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.36 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS b 79 PHE 0.014 0.001 PHE b 62 TYR 0.050 0.002 TYR O 88 ARG 0.006 0.000 ARG M 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 270 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8906 (tptt) cc_final: 0.8640 (tppt) REVERT: H 32 GLU cc_start: 0.8078 (pp20) cc_final: 0.7852 (pp20) REVERT: H 87 THR cc_start: 0.8038 (p) cc_final: 0.7650 (p) REVERT: H 92 GLN cc_start: 0.8470 (tp40) cc_final: 0.7929 (tp40) REVERT: H 102 GLU cc_start: 0.8065 (pp20) cc_final: 0.7751 (pp20) REVERT: M 131 ARG cc_start: 0.7926 (ptp-170) cc_final: 0.7451 (ptm160) REVERT: a 42 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7662 (ttp80) REVERT: a 65 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8156 (mm) REVERT: a 95 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8961 (mtpp) REVERT: b 64 ASN cc_start: 0.8727 (m-40) cc_final: 0.8488 (m110) REVERT: b 76 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8415 (ttm110) REVERT: b 113 LYS cc_start: 0.7717 (pptt) cc_final: 0.7466 (pttp) REVERT: h 35 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8011 (mmm-85) REVERT: h 66 ILE cc_start: 0.8945 (pt) cc_final: 0.8496 (mt) REVERT: k 35 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8388 (mpp80) REVERT: k 91 GLU cc_start: 0.8396 (pp20) cc_final: 0.7869 (pp20) outliers start: 29 outliers final: 21 residues processed: 281 average time/residue: 0.2980 time to fit residues: 110.6983 Evaluate side-chains 270 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 0.0000 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN a 38 ASN ** a 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 HIS ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 GLN k 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12721 Z= 0.199 Angle : 0.708 12.693 18448 Z= 0.398 Chirality : 0.037 0.183 2104 Planarity : 0.005 0.058 1319 Dihedral : 31.796 88.150 4127 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.19 % Allowed : 36.16 % Favored : 57.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 730 helix: 0.95 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.30 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS b 79 PHE 0.019 0.002 PHE O 61 TYR 0.048 0.003 TYR h 88 ARG 0.005 0.000 ARG M 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 GLU cc_start: 0.8087 (pp20) cc_final: 0.7732 (pp20) REVERT: H 98 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7942 (tt) REVERT: H 102 GLU cc_start: 0.8094 (pp20) cc_final: 0.7799 (pp20) REVERT: a 33 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9051 (mm) REVERT: a 42 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7715 (ttp80) REVERT: a 65 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8238 (mm) REVERT: a 95 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8964 (mtpp) REVERT: b 64 ASN cc_start: 0.8733 (m-40) cc_final: 0.8492 (m110) REVERT: b 76 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8446 (ttm110) REVERT: b 113 LYS cc_start: 0.7697 (pptt) cc_final: 0.7459 (pttp) REVERT: h 66 ILE cc_start: 0.8959 (pt) cc_final: 0.8580 (mt) REVERT: k 35 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8365 (mpp80) REVERT: k 91 GLU cc_start: 0.8432 (pp20) cc_final: 0.7845 (pp20) outliers start: 38 outliers final: 28 residues processed: 271 average time/residue: 0.2881 time to fit residues: 103.4911 Evaluate side-chains 271 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 95 LYS Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** a 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 GLN k 38 ASN ** k 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12721 Z= 0.197 Angle : 0.717 12.564 18448 Z= 0.400 Chirality : 0.037 0.192 2104 Planarity : 0.005 0.058 1319 Dihedral : 31.789 88.545 4127 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.84 % Allowed : 35.67 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 730 helix: 0.99 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.29 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 75 PHE 0.020 0.002 PHE O 61 TYR 0.052 0.003 TYR O 88 ARG 0.006 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 263 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 GLU cc_start: 0.8095 (pp20) cc_final: 0.7652 (pp20) REVERT: H 98 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7946 (tt) REVERT: H 102 GLU cc_start: 0.8084 (pp20) cc_final: 0.7805 (pp20) REVERT: H 108 VAL cc_start: 0.9201 (m) cc_final: 0.8997 (p) REVERT: M 131 ARG cc_start: 0.7939 (ptm-80) cc_final: 0.7688 (ptm-80) REVERT: a 42 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7779 (ttp80) REVERT: a 65 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8217 (mm) REVERT: a 95 LYS cc_start: 0.9252 (ttmm) cc_final: 0.8941 (mtpp) REVERT: b 64 ASN cc_start: 0.8734 (m-40) cc_final: 0.8499 (m110) REVERT: b 76 ARG cc_start: 0.8914 (ttm110) cc_final: 0.8485 (ttm110) REVERT: b 113 LYS cc_start: 0.7718 (pptt) cc_final: 0.7470 (pttp) REVERT: h 66 ILE cc_start: 0.8943 (pt) cc_final: 0.8496 (mt) REVERT: k 32 ARG cc_start: 0.8656 (tmm-80) cc_final: 0.8040 (tmm-80) REVERT: k 35 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8343 (mpp80) REVERT: k 71 ARG cc_start: 0.8945 (mtm110) cc_final: 0.8611 (mtt90) REVERT: k 91 GLU cc_start: 0.8463 (pp20) cc_final: 0.7869 (pp20) outliers start: 42 outliers final: 31 residues processed: 280 average time/residue: 0.3071 time to fit residues: 114.2399 Evaluate side-chains 281 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN a 38 ASN a 73 ASN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 GLN k 38 ASN k 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12721 Z= 0.225 Angle : 0.745 14.647 18448 Z= 0.411 Chirality : 0.037 0.190 2104 Planarity : 0.005 0.060 1319 Dihedral : 31.894 89.620 4127 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 7.00 % Allowed : 36.81 % Favored : 56.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 730 helix: 0.96 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.29 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 75 PHE 0.023 0.002 PHE O 61 TYR 0.051 0.003 TYR O 88 ARG 0.008 0.001 ARG b 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 GLU cc_start: 0.8095 (pp20) cc_final: 0.7708 (pp20) REVERT: H 98 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7879 (tt) REVERT: a 42 ARG cc_start: 0.8056 (mmm-85) cc_final: 0.7853 (ttp80) REVERT: a 65 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8254 (mm) REVERT: a 112 GLN cc_start: 0.6960 (tp-100) cc_final: 0.6703 (tp-100) REVERT: b 30 ARG cc_start: 0.6818 (tpp-160) cc_final: 0.6567 (mmp80) REVERT: b 64 ASN cc_start: 0.8749 (m-40) cc_final: 0.8508 (m110) REVERT: b 76 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8508 (ttm110) REVERT: b 113 LYS cc_start: 0.7807 (pptt) cc_final: 0.7567 (pttp) REVERT: f 59 GLU cc_start: 0.8120 (tp30) cc_final: 0.7837 (tp30) REVERT: h 66 ILE cc_start: 0.8973 (pt) cc_final: 0.8578 (mt) REVERT: h 72 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.7186 (t80) REVERT: k 23 LEU cc_start: 0.7577 (mt) cc_final: 0.7102 (mp) REVERT: k 24 GLN cc_start: 0.6790 (tp40) cc_final: 0.5835 (tt0) REVERT: k 35 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8354 (mpp80) REVERT: k 91 GLU cc_start: 0.8503 (pp20) cc_final: 0.7874 (pp20) REVERT: k 92 GLU cc_start: 0.8144 (pm20) cc_final: 0.7933 (pm20) outliers start: 43 outliers final: 34 residues processed: 271 average time/residue: 0.2924 time to fit residues: 106.4624 Evaluate side-chains 279 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 76 THR Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0470 chunk 91 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12721 Z= 0.201 Angle : 0.756 14.792 18448 Z= 0.412 Chirality : 0.037 0.201 2104 Planarity : 0.005 0.062 1319 Dihedral : 31.845 89.300 4127 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.37 % Allowed : 39.09 % Favored : 55.54 % 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: 0.51 (0.30), residues: 730 helix: 1.00 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.36 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 75 PHE 0.023 0.002 PHE O 61 TYR 0.051 0.003 TYR O 88 ARG 0.007 0.001 ARG h 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 98 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7925 (tt) REVERT: M 122 LYS cc_start: 0.8367 (pttp) cc_final: 0.8145 (ptmt) REVERT: a 42 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7882 (ttp80) REVERT: a 65 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8187 (mm) REVERT: b 64 ASN cc_start: 0.8735 (m-40) cc_final: 0.8502 (m110) REVERT: b 76 ARG cc_start: 0.8854 (ttm110) cc_final: 0.8482 (ttm110) REVERT: b 113 LYS cc_start: 0.7788 (pptt) cc_final: 0.7526 (pttp) REVERT: f 83 ARG cc_start: 0.8291 (mmp80) cc_final: 0.7958 (mmm160) REVERT: h 66 ILE cc_start: 0.8930 (pt) cc_final: 0.8489 (mt) REVERT: h 72 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7129 (t80) REVERT: k 23 LEU cc_start: 0.7368 (mt) cc_final: 0.6954 (mp) REVERT: k 24 GLN cc_start: 0.6892 (tp40) cc_final: 0.6237 (tt0) REVERT: k 35 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8389 (mpp80) REVERT: k 91 GLU cc_start: 0.8495 (pp20) cc_final: 0.7850 (pp20) REVERT: k 92 GLU cc_start: 0.8221 (pm20) cc_final: 0.7962 (pm20) outliers start: 33 outliers final: 26 residues processed: 268 average time/residue: 0.2798 time to fit residues: 100.8088 Evaluate side-chains 276 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 246 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 ASN ** k 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12721 Z= 0.243 Angle : 0.776 14.331 18448 Z= 0.424 Chirality : 0.039 0.291 2104 Planarity : 0.005 0.061 1319 Dihedral : 31.890 89.819 4127 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.19 % Allowed : 38.93 % Favored : 54.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.30), residues: 730 helix: 0.89 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS h 75 PHE 0.028 0.002 PHE O 61 TYR 0.051 0.003 TYR O 88 ARG 0.009 0.001 ARG b 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 245 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 98 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7844 (tt) REVERT: M 122 LYS cc_start: 0.8389 (pttp) cc_final: 0.8186 (ptmt) REVERT: a 33 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9053 (mm) REVERT: a 65 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8259 (mm) REVERT: b 64 ASN cc_start: 0.8750 (m-40) cc_final: 0.8471 (m110) REVERT: b 76 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8505 (ttm110) REVERT: b 113 LYS cc_start: 0.7770 (pptt) cc_final: 0.7513 (pttp) REVERT: h 66 ILE cc_start: 0.8996 (pt) cc_final: 0.8538 (mt) REVERT: h 72 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7138 (t80) REVERT: k 23 LEU cc_start: 0.7604 (mt) cc_final: 0.7203 (mp) REVERT: k 24 GLN cc_start: 0.7017 (tp40) cc_final: 0.6313 (tt0) REVERT: k 32 ARG cc_start: 0.8995 (tmm-80) cc_final: 0.8715 (tmm-80) REVERT: k 35 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8397 (mpp80) outliers start: 38 outliers final: 32 residues processed: 259 average time/residue: 0.2755 time to fit residues: 96.0136 Evaluate side-chains 278 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 241 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 38 ASN Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 48 ASP Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 72 TYR Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.095617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.076655 restraints weight = 48888.414| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.06 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 12721 Z= 0.294 Angle : 1.109 59.177 18448 Z= 0.660 Chirality : 0.048 0.919 2104 Planarity : 0.006 0.061 1319 Dihedral : 31.887 89.845 4127 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.19 % Allowed : 38.27 % Favored : 55.54 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.30), residues: 730 helix: 0.88 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.29 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS h 75 PHE 0.025 0.002 PHE O 61 TYR 0.050 0.003 TYR O 88 ARG 0.010 0.001 ARG a 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2904.28 seconds wall clock time: 53 minutes 7.69 seconds (3187.69 seconds total)