Starting phenix.real_space_refine on Mon Sep 30 00:14:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/09_2024/6pwx_20514.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/09_2024/6pwx_20514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/09_2024/6pwx_20514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/09_2024/6pwx_20514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/09_2024/6pwx_20514.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/09_2024/6pwx_20514.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11964 atoms to isotropic. 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 27 5.16 5 C 8152 2.51 5 N 2673 2.21 5 O 3267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.85s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14411 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2447 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 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: "H" 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: "I" 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: "J" 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: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 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: "M" 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: "N" 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: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" 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 Time building chain proxies: 8.98, per 1000 atoms: 0.62 Number of scatterers: 14411 At special positions: 0 Unit cell: (102.01, 129.28, 123.22, 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 27 16.00 P 292 15.00 O 3267 8.00 N 2673 7.00 C 8152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 945.4 milliseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 51.7% alpha, 12.1% beta 147 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'H' and resid 24 through 29 removed outlier: 4.311A pdb=" N GLN H 27 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.951A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.534A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.339A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 removed outlier: 3.562A pdb=" N ASN I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 100 through 120 removed outlier: 3.685A pdb=" N ALA J 104 " --> pdb=" O PRO J 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.484A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 101 through 121 removed outlier: 3.863A pdb=" N ALA N 121 " --> pdb=" O LYS N 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.310A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.951A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.533A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.394A pdb=" N VAL A 318 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 309 " --> pdb=" O TRP A 303 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP A 303 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 311 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 301 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 313 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.652A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 7.102A pdb=" N ALA A 84 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 72 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 82 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP A 74 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 80 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP A 94 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 100 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 115 removed outlier: 4.062A pdb=" N LYS A 112 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 159 removed outlier: 6.976A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.142A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.050A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.169A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.382A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.055A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 77 through 78 479 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 5.91 Time building geometry restraints manager: 4.28 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: 3042 1.33 - 1.45: 4521 1.45 - 1.57: 7085 1.57 - 1.69: 582 1.69 - 1.81: 41 Bond restraints: 15271 Sorted by residual: bond pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" C3' DC P 126 " pdb=" O3' DC P 126 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CG GLU H 52 " pdb=" CD GLU H 52 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG ASP K 106 " pdb=" OD1 ASP K 106 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.41e+00 ... (remaining 15266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 21339 1.65 - 3.29: 541 3.29 - 4.94: 24 4.94 - 6.58: 7 6.58 - 8.23: 4 Bond angle restraints: 21915 Sorted by residual: angle pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " pdb=" CD GLU H 52 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.70e+00 3.46e-01 1.34e+01 angle pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " pdb=" CD GLU L 52 " ideal model delta sigma weight residual 112.60 118.76 -6.16 1.70e+00 3.46e-01 1.32e+01 angle pdb=" N ASP G 106 " pdb=" CA ASP G 106 " pdb=" CB ASP G 106 " ideal model delta sigma weight residual 110.28 115.41 -5.13 1.55e+00 4.16e-01 1.10e+01 ... (remaining 21910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.55: 6405 26.55 - 53.09: 1583 53.09 - 79.64: 404 79.64 - 106.18: 13 106.18 - 132.73: 3 Dihedral angle restraints: 8408 sinusoidal: 5295 harmonic: 3113 Sorted by residual: dihedral pdb=" CA ILE L 50 " pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE H 50 " pdb=" C ILE H 50 " pdb=" N TYR H 51 " pdb=" CA TYR H 51 " ideal model delta harmonic sigma weight residual 180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C4' DG P 94 " pdb=" C3' DG P 94 " pdb=" O3' DG P 94 " pdb=" P DG P 95 " ideal model delta sinusoidal sigma weight residual -140.00 -7.27 -132.73 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 8405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1634 0.028 - 0.057: 609 0.057 - 0.085: 165 0.085 - 0.113: 84 0.113 - 0.141: 17 Chirality restraints: 2509 Sorted by residual: chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL A 125 " pdb=" N VAL A 125 " pdb=" C VAL A 125 " pdb=" CB VAL A 125 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2506 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 64 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C ASN L 64 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN L 64 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL L 65 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 64 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASN H 64 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN H 64 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL H 65 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 80 " -0.007 2.00e-02 2.50e+03 1.33e-02 4.00e+00 pdb=" N1 DC O 80 " 0.013 2.00e-02 2.50e+03 pdb=" C2 DC O 80 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DC O 80 " -0.018 2.00e-02 2.50e+03 pdb=" N3 DC O 80 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC O 80 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC O 80 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC O 80 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC O 80 " -0.006 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 419 2.66 - 3.22: 13370 3.22 - 3.78: 29040 3.78 - 4.34: 34913 4.34 - 4.90: 49905 Nonbonded interactions: 127647 Sorted by model distance: nonbonded pdb=" N2 DG O 83 " pdb=" O2 DC P 65 " model vdw 2.098 2.496 nonbonded pdb=" OG1 THR A 217 " pdb=" OD1 ASP A 219 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLU L 52 " pdb=" N GLU L 53 " model vdw 2.219 3.120 nonbonded pdb=" OE1 GLU H 52 " pdb=" N GLU H 53 " model vdw 2.220 3.120 nonbonded pdb=" OP1 DA P 102 " pdb=" N LYS L 79 " model vdw 2.236 3.120 ... (remaining 127642 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 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' 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 'M' 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 'J' selection = (chain 'N' 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 group one per residue 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: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.390 Find NCS groups from input model: 0.310 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.003 0.048 15271 Z= 0.174 Angle : 0.591 8.229 21915 Z= 0.368 Chirality : 0.036 0.141 2509 Planarity : 0.003 0.038 1765 Dihedral : 27.209 132.729 6396 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.58 % Allowed : 3.80 % Favored : 92.62 % 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: -1.76 (0.24), residues: 1056 helix: -0.03 (0.20), residues: 546 sheet: -2.08 (0.44), residues: 134 loop : -2.45 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 279 HIS 0.003 0.001 HIS H 75 PHE 0.006 0.001 PHE H 100 TYR 0.008 0.001 TYR I 57 ARG 0.002 0.000 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 427 time to evaluate : 1.173 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: symmetry clash REVERT: A 53 PHE cc_start: 0.8503 (m-80) cc_final: 0.8185 (m-80) REVERT: A 81 LEU cc_start: 0.8838 (mt) cc_final: 0.8470 (pp) REVERT: A 134 MET cc_start: 0.8204 (ttp) cc_final: 0.6763 (mpp) REVERT: A 251 ARG cc_start: 0.8917 (mmt90) cc_final: 0.8545 (mmt180) REVERT: A 264 GLU cc_start: 0.7380 (tp30) cc_final: 0.7142 (tp30) REVERT: A 265 TYR cc_start: 0.7885 (m-10) cc_final: 0.7662 (m-10) REVERT: G 41 TYR cc_start: 0.8597 (m-80) cc_final: 0.8208 (m-80) REVERT: G 77 ASP cc_start: 0.9475 (OUTLIER) cc_final: 0.8920 (t70) REVERT: G 93 GLN cc_start: 0.9191 (tt0) cc_final: 0.8739 (tt0) REVERT: G 106 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8764 (p0) REVERT: G 107 THR cc_start: 0.9431 (p) cc_final: 0.8885 (p) REVERT: G 123 ASP cc_start: 0.8536 (t70) cc_final: 0.6797 (t70) REVERT: G 124 ILE cc_start: 0.9596 (mt) cc_final: 0.9288 (tp) REVERT: G 125 GLN cc_start: 0.9126 (mt0) cc_final: 0.8763 (mt0) REVERT: H 22 LEU cc_start: 0.7817 (mm) cc_final: 0.7131 (mm) REVERT: H 39 ARG cc_start: 0.9191 (mmt-90) cc_final: 0.8838 (tpp-160) REVERT: H 43 VAL cc_start: 0.8535 (t) cc_final: 0.7835 (t) REVERT: H 51 TYR cc_start: 0.8158 (m-80) cc_final: 0.6959 (m-10) REVERT: H 55 ARG cc_start: 0.9131 (mtt90) cc_final: 0.8756 (mtm-85) REVERT: H 64 ASN cc_start: 0.9109 (m-40) cc_final: 0.8686 (m-40) REVERT: H 75 HIS cc_start: 0.8678 (t70) cc_final: 0.8356 (t-90) REVERT: H 77 LYS cc_start: 0.9483 (mttt) cc_final: 0.9192 (mmtm) REVERT: I 42 ARG cc_start: 0.9350 (mtm180) cc_final: 0.8922 (ttm110) REVERT: I 61 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8814 (tp30) REVERT: I 75 LYS cc_start: 0.9360 (mmtm) cc_final: 0.8983 (mmtp) REVERT: I 76 THR cc_start: 0.9233 (m) cc_final: 0.8920 (p) REVERT: I 84 GLN cc_start: 0.9603 (tp40) cc_final: 0.9402 (tp40) REVERT: I 94 ASN cc_start: 0.9066 (t0) cc_final: 0.8524 (t0) REVERT: I 95 LYS cc_start: 0.9580 (tptt) cc_final: 0.9298 (tppt) REVERT: I 104 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8584 (mp10) REVERT: J 32 GLU cc_start: 0.9040 (pp20) cc_final: 0.8318 (pp20) REVERT: J 40 LYS cc_start: 0.9651 (mttt) cc_final: 0.9331 (mtpt) REVERT: J 62 PHE cc_start: 0.9567 (t80) cc_final: 0.9154 (t80) REVERT: J 65 ASP cc_start: 0.8605 (t70) cc_final: 0.7657 (t0) REVERT: J 68 GLU cc_start: 0.9083 (tp30) cc_final: 0.8737 (tp30) REVERT: J 76 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8763 (ttm110) REVERT: J 81 ASN cc_start: 0.9278 (m-40) cc_final: 0.8398 (m-40) REVERT: J 85 THR cc_start: 0.8640 (p) cc_final: 0.8385 (p) REVERT: J 90 GLU cc_start: 0.9256 (mp0) cc_final: 0.9041 (mp0) REVERT: J 93 THR cc_start: 0.9750 (m) cc_final: 0.9500 (p) REVERT: J 102 GLU cc_start: 0.8794 (tp30) cc_final: 0.8568 (tm-30) REVERT: J 103 LEU cc_start: 0.9338 (mt) cc_final: 0.9102 (mt) REVERT: J 110 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9001 (mm-30) REVERT: K 48 LEU cc_start: 0.9613 (mp) cc_final: 0.9275 (mp) REVERT: K 50 GLU cc_start: 0.8350 (tp30) cc_final: 0.7679 (tp30) REVERT: K 52 ARG cc_start: 0.9252 (mtt90) cc_final: 0.8808 (mtm-85) REVERT: K 54 TYR cc_start: 0.8942 (m-10) cc_final: 0.8680 (m-10) REVERT: K 60 LEU cc_start: 0.9241 (mt) cc_final: 0.8956 (mt) REVERT: K 65 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9257 (tp) REVERT: K 67 PHE cc_start: 0.9575 (t80) cc_final: 0.9359 (t80) REVERT: K 68 GLN cc_start: 0.9305 (tt0) cc_final: 0.9000 (tt0) REVERT: K 86 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8303 (t) REVERT: K 93 GLN cc_start: 0.9622 (tt0) cc_final: 0.9393 (tm-30) REVERT: K 94 GLU cc_start: 0.9367 (tt0) cc_final: 0.9164 (tm-30) REVERT: K 123 ASP cc_start: 0.7897 (t70) cc_final: 0.6271 (t70) REVERT: M 36 LYS cc_start: 0.9139 (mttm) cc_final: 0.8822 (tttt) REVERT: M 42 ARG cc_start: 0.9210 (ptm160) cc_final: 0.8747 (ptm160) REVERT: M 64 GLU cc_start: 0.9463 (tt0) cc_final: 0.8913 (tm-30) REVERT: M 68 ASN cc_start: 0.9462 (m-40) cc_final: 0.8186 (m-40) REVERT: M 78 ILE cc_start: 0.9640 (mt) cc_final: 0.9403 (mm) REVERT: M 112 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8623 (mp10) REVERT: N 65 ASP cc_start: 0.9313 (t0) cc_final: 0.8889 (t0) REVERT: N 91 ILE cc_start: 0.9716 (mm) cc_final: 0.9316 (tt) REVERT: N 96 ARG cc_start: 0.9129 (mtp180) cc_final: 0.8600 (ttm110) REVERT: N 97 LEU cc_start: 0.9438 (mt) cc_final: 0.9097 (mt) REVERT: N 105 LYS cc_start: 0.9155 (mttt) cc_final: 0.8455 (mtpp) REVERT: N 110 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8409 (mt-10) REVERT: L 25 ASN cc_start: 0.8035 (t0) cc_final: 0.6719 (t0) REVERT: L 51 TYR cc_start: 0.8022 (m-80) cc_final: 0.7624 (m-80) REVERT: L 79 LYS cc_start: 0.8682 (mmtt) cc_final: 0.7922 (mmmt) REVERT: L 82 THR cc_start: 0.9304 (p) cc_final: 0.9058 (p) REVERT: L 98 TYR cc_start: 0.8930 (m-10) cc_final: 0.8041 (m-80) outliers start: 32 outliers final: 11 residues processed: 436 average time/residue: 0.3160 time to fit residues: 186.0103 Evaluate side-chains 350 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 335 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 197 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 68 GLN H 25 ASN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN K 76 GLN K 108 ASN N 46 HIS L 25 ASN L 64 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15271 Z= 0.273 Angle : 0.633 8.212 21915 Z= 0.364 Chirality : 0.038 0.174 2509 Planarity : 0.005 0.075 1765 Dihedral : 30.369 132.028 4372 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: -0.52 (0.25), residues: 1056 helix: 1.03 (0.21), residues: 554 sheet: -1.97 (0.44), residues: 139 loop : -1.80 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 35 HIS 0.007 0.001 HIS H 75 PHE 0.029 0.002 PHE G 67 TYR 0.026 0.002 TYR H 88 ARG 0.006 0.001 ARG M 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.212 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8874 (mt) cc_final: 0.8554 (pp) REVERT: A 134 MET cc_start: 0.8136 (ttp) cc_final: 0.6700 (mpp) REVERT: A 225 TYR cc_start: 0.7191 (m-80) cc_final: 0.6894 (m-80) REVERT: A 251 ARG cc_start: 0.9015 (mmt90) cc_final: 0.8577 (mmt180) REVERT: A 265 TYR cc_start: 0.7730 (m-10) cc_final: 0.7524 (m-10) REVERT: A 280 GLU cc_start: 0.8464 (tt0) cc_final: 0.8207 (tt0) REVERT: G 41 TYR cc_start: 0.8749 (m-80) cc_final: 0.8299 (m-80) REVERT: G 50 GLU cc_start: 0.8554 (tp30) cc_final: 0.8267 (tp30) REVERT: G 51 ILE cc_start: 0.9461 (mt) cc_final: 0.9175 (mm) REVERT: G 60 LEU cc_start: 0.9302 (mp) cc_final: 0.8786 (mp) REVERT: G 77 ASP cc_start: 0.8997 (t70) cc_final: 0.8682 (t70) REVERT: G 93 GLN cc_start: 0.9415 (tt0) cc_final: 0.9049 (tm-30) REVERT: G 122 LYS cc_start: 0.8874 (ptmt) cc_final: 0.8557 (ptpt) REVERT: G 125 GLN cc_start: 0.9188 (mt0) cc_final: 0.8755 (mt0) REVERT: H 22 LEU cc_start: 0.7857 (mm) cc_final: 0.7196 (mm) REVERT: H 25 ASN cc_start: 0.8399 (t0) cc_final: 0.7657 (t0) REVERT: H 30 THR cc_start: 0.9205 (p) cc_final: 0.8807 (t) REVERT: H 51 TYR cc_start: 0.8164 (m-80) cc_final: 0.7883 (m-80) REVERT: H 74 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8999 (mt-10) REVERT: I 42 ARG cc_start: 0.9373 (mtm180) cc_final: 0.8945 (ttm110) REVERT: I 61 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9054 (mm-30) REVERT: I 68 ASN cc_start: 0.9337 (m-40) cc_final: 0.9121 (m110) REVERT: I 75 LYS cc_start: 0.9458 (mmtm) cc_final: 0.9008 (mmtp) REVERT: I 76 THR cc_start: 0.9290 (m) cc_final: 0.8966 (p) REVERT: I 87 VAL cc_start: 0.9577 (m) cc_final: 0.9330 (m) REVERT: I 90 ASP cc_start: 0.9241 (t70) cc_final: 0.8999 (t0) REVERT: I 94 ASN cc_start: 0.9056 (t0) cc_final: 0.8556 (t0) REVERT: I 95 LYS cc_start: 0.9615 (tptt) cc_final: 0.9359 (tppt) REVERT: J 32 GLU cc_start: 0.9125 (pp20) cc_final: 0.8347 (pp20) REVERT: J 44 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8892 (tm-30) REVERT: J 56 MET cc_start: 0.9377 (tpp) cc_final: 0.9153 (tpp) REVERT: J 65 ASP cc_start: 0.8811 (t70) cc_final: 0.8375 (t0) REVERT: J 68 GLU cc_start: 0.9169 (tp30) cc_final: 0.8885 (tp30) REVERT: J 73 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8848 (mm-30) REVERT: J 76 ARG cc_start: 0.9241 (ttm110) cc_final: 0.8731 (ttm110) REVERT: J 81 ASN cc_start: 0.9242 (m-40) cc_final: 0.8147 (p0) REVERT: J 85 THR cc_start: 0.8740 (p) cc_final: 0.8303 (p) REVERT: J 93 THR cc_start: 0.9754 (m) cc_final: 0.9507 (p) REVERT: J 98 LEU cc_start: 0.9035 (tt) cc_final: 0.8697 (tt) REVERT: K 50 GLU cc_start: 0.8348 (tp30) cc_final: 0.7675 (tp30) REVERT: K 54 TYR cc_start: 0.8844 (m-10) cc_final: 0.8640 (m-10) REVERT: K 85 GLN cc_start: 0.9413 (mm110) cc_final: 0.9190 (mm110) REVERT: K 90 MET cc_start: 0.8920 (ptp) cc_final: 0.8656 (ptp) REVERT: K 93 GLN cc_start: 0.9568 (tt0) cc_final: 0.9285 (tm-30) REVERT: K 120 MET cc_start: 0.9164 (mmp) cc_final: 0.8807 (mmm) REVERT: K 123 ASP cc_start: 0.7033 (t70) cc_final: 0.6819 (t70) REVERT: M 36 LYS cc_start: 0.9211 (mttm) cc_final: 0.8844 (pttt) REVERT: M 56 GLU cc_start: 0.9457 (tt0) cc_final: 0.9114 (mt-10) REVERT: M 57 TYR cc_start: 0.9445 (t80) cc_final: 0.9059 (t80) REVERT: M 64 GLU cc_start: 0.9452 (tt0) cc_final: 0.8946 (tm-30) REVERT: M 68 ASN cc_start: 0.9526 (m-40) cc_final: 0.8241 (m-40) REVERT: M 93 LEU cc_start: 0.9659 (tp) cc_final: 0.9423 (tt) REVERT: M 112 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8712 (mp10) REVERT: N 44 GLN cc_start: 0.9419 (tm-30) cc_final: 0.9055 (tm-30) REVERT: N 56 MET cc_start: 0.9267 (tpt) cc_final: 0.9004 (tpp) REVERT: N 65 ASP cc_start: 0.9432 (t0) cc_final: 0.8960 (t0) REVERT: N 86 ILE cc_start: 0.9236 (mt) cc_final: 0.8837 (mt) REVERT: N 90 GLU cc_start: 0.9167 (mp0) cc_final: 0.8806 (mp0) REVERT: N 96 ARG cc_start: 0.9003 (mtp180) cc_final: 0.8275 (ttm110) REVERT: N 110 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8565 (mt-10) REVERT: L 43 VAL cc_start: 0.9753 (t) cc_final: 0.9452 (m) REVERT: L 51 TYR cc_start: 0.8567 (m-80) cc_final: 0.8184 (m-80) REVERT: L 63 GLU cc_start: 0.9038 (tp30) cc_final: 0.8803 (tp30) REVERT: L 88 TYR cc_start: 0.9446 (m-10) cc_final: 0.8979 (m-10) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2664 time to fit residues: 138.9618 Evaluate side-chains 309 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15271 Z= 0.279 Angle : 0.625 6.905 21915 Z= 0.362 Chirality : 0.039 0.200 2509 Planarity : 0.005 0.060 1765 Dihedral : 30.245 133.279 4372 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.11 % Allowed : 2.91 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1056 helix: 1.46 (0.21), residues: 536 sheet: -1.73 (0.43), residues: 144 loop : -1.69 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 51 HIS 0.008 0.001 HIS H 75 PHE 0.030 0.002 PHE K 67 TYR 0.038 0.002 TYR H 88 ARG 0.005 0.001 ARG L 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 1.203 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: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8505 (mtp) cc_final: 0.8142 (mtp) REVERT: A 81 LEU cc_start: 0.8846 (mt) cc_final: 0.8582 (pp) REVERT: A 134 MET cc_start: 0.8116 (ttp) cc_final: 0.6674 (mpp) REVERT: A 251 ARG cc_start: 0.9028 (mmt90) cc_final: 0.8591 (mmt180) REVERT: A 259 PHE cc_start: 0.6594 (m-80) cc_final: 0.5685 (m-80) REVERT: A 265 TYR cc_start: 0.7650 (m-80) cc_final: 0.7370 (m-10) REVERT: A 280 GLU cc_start: 0.8608 (tt0) cc_final: 0.8236 (tt0) REVERT: G 50 GLU cc_start: 0.8472 (tp30) cc_final: 0.8184 (tp30) REVERT: G 60 LEU cc_start: 0.9319 (mp) cc_final: 0.8635 (mp) REVERT: G 63 ARG cc_start: 0.8186 (mmt-90) cc_final: 0.7721 (mmm-85) REVERT: G 73 GLU cc_start: 0.8974 (tt0) cc_final: 0.8372 (tt0) REVERT: G 77 ASP cc_start: 0.9149 (t70) cc_final: 0.8788 (t70) REVERT: G 85 GLN cc_start: 0.9209 (mt0) cc_final: 0.9001 (mt0) REVERT: G 93 GLN cc_start: 0.9440 (tt0) cc_final: 0.9060 (tm-30) REVERT: G 113 HIS cc_start: 0.8864 (t-170) cc_final: 0.8653 (t-170) REVERT: G 122 LYS cc_start: 0.8881 (ptmt) cc_final: 0.8576 (ptpt) REVERT: G 125 GLN cc_start: 0.9182 (mt0) cc_final: 0.8786 (pt0) REVERT: H 25 ASN cc_start: 0.8661 (t160) cc_final: 0.8120 (m-40) REVERT: H 30 THR cc_start: 0.9303 (p) cc_final: 0.8845 (t) REVERT: H 43 VAL cc_start: 0.9505 (t) cc_final: 0.9085 (p) REVERT: H 68 ASP cc_start: 0.9293 (m-30) cc_final: 0.8905 (m-30) REVERT: H 74 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8807 (tm-30) REVERT: I 61 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9006 (mm-30) REVERT: I 68 ASN cc_start: 0.9350 (m-40) cc_final: 0.9145 (m110) REVERT: I 73 ASN cc_start: 0.9342 (t0) cc_final: 0.9041 (t0) REVERT: I 75 LYS cc_start: 0.9478 (mmtm) cc_final: 0.9043 (mmtp) REVERT: I 76 THR cc_start: 0.9344 (m) cc_final: 0.8983 (p) REVERT: I 87 VAL cc_start: 0.9564 (m) cc_final: 0.9325 (m) REVERT: I 90 ASP cc_start: 0.9027 (t70) cc_final: 0.8628 (t0) REVERT: I 94 ASN cc_start: 0.9007 (t0) cc_final: 0.8503 (t0) REVERT: I 95 LYS cc_start: 0.9627 (tptt) cc_final: 0.9344 (tppt) REVERT: J 32 GLU cc_start: 0.9181 (pp20) cc_final: 0.8832 (pp20) REVERT: J 44 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8740 (tm-30) REVERT: J 56 MET cc_start: 0.9308 (tpp) cc_final: 0.9080 (tpp) REVERT: J 65 ASP cc_start: 0.8964 (t70) cc_final: 0.8665 (t70) REVERT: J 73 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8776 (mm-30) REVERT: J 76 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8837 (ttm110) REVERT: J 81 ASN cc_start: 0.9168 (m-40) cc_final: 0.8140 (p0) REVERT: J 93 THR cc_start: 0.9743 (m) cc_final: 0.9520 (p) REVERT: J 98 LEU cc_start: 0.9162 (tt) cc_final: 0.8863 (tt) REVERT: K 41 TYR cc_start: 0.8954 (m-80) cc_final: 0.8651 (m-80) REVERT: K 50 GLU cc_start: 0.8361 (tp30) cc_final: 0.7922 (tp30) REVERT: K 52 ARG cc_start: 0.9291 (mtt90) cc_final: 0.8924 (mtm-85) REVERT: K 54 TYR cc_start: 0.8840 (m-10) cc_final: 0.8622 (m-10) REVERT: K 60 LEU cc_start: 0.9084 (mt) cc_final: 0.8822 (pt) REVERT: K 64 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8728 (pttt) REVERT: K 65 LEU cc_start: 0.9692 (mp) cc_final: 0.9479 (mp) REVERT: K 73 GLU cc_start: 0.8168 (pt0) cc_final: 0.7925 (pt0) REVERT: K 85 GLN cc_start: 0.9354 (mm110) cc_final: 0.9127 (mm110) REVERT: K 93 GLN cc_start: 0.9599 (tt0) cc_final: 0.9391 (tm-30) REVERT: K 97 GLU cc_start: 0.9293 (tt0) cc_final: 0.8787 (tt0) REVERT: K 120 MET cc_start: 0.9373 (mmp) cc_final: 0.8901 (mmm) REVERT: K 124 ILE cc_start: 0.9486 (mm) cc_final: 0.9259 (mm) REVERT: M 35 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: M 36 LYS cc_start: 0.9195 (mttm) cc_final: 0.8816 (pttt) REVERT: M 64 GLU cc_start: 0.9466 (tt0) cc_final: 0.8959 (tm-30) REVERT: M 68 ASN cc_start: 0.9495 (m-40) cc_final: 0.8158 (m-40) REVERT: M 112 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8600 (mp10) REVERT: N 34 TYR cc_start: 0.9611 (m-80) cc_final: 0.9389 (m-80) REVERT: N 43 LYS cc_start: 0.9611 (tppp) cc_final: 0.9383 (tppp) REVERT: N 44 GLN cc_start: 0.9422 (tm-30) cc_final: 0.9096 (tm-30) REVERT: N 65 ASP cc_start: 0.9429 (t0) cc_final: 0.8904 (t0) REVERT: N 83 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8499 (mmm160) REVERT: N 96 ARG cc_start: 0.9114 (mtp180) cc_final: 0.8383 (ttm110) REVERT: N 110 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8608 (mt-10) REVERT: L 43 VAL cc_start: 0.9729 (t) cc_final: 0.9491 (m) REVERT: L 53 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8120 (tm-30) REVERT: L 63 GLU cc_start: 0.9096 (tp30) cc_final: 0.8723 (tp30) REVERT: L 74 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8969 (tm-30) REVERT: L 79 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8123 (mmtm) REVERT: L 88 TYR cc_start: 0.9490 (m-10) cc_final: 0.9081 (m-10) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.2938 time to fit residues: 150.1085 Evaluate side-chains 311 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 76 GLN G 108 ASN G 113 HIS H 25 ASN K 125 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15271 Z= 0.196 Angle : 0.598 7.510 21915 Z= 0.348 Chirality : 0.037 0.157 2509 Planarity : 0.004 0.057 1765 Dihedral : 30.099 133.856 4372 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 0.03 (0.26), residues: 1056 helix: 1.53 (0.21), residues: 546 sheet: -1.67 (0.42), residues: 155 loop : -1.55 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 279 HIS 0.009 0.001 HIS L 75 PHE 0.018 0.002 PHE A 206 TYR 0.048 0.002 TYR H 88 ARG 0.005 0.000 ARG L 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8467 (mtp) cc_final: 0.8237 (mmp) REVERT: A 81 LEU cc_start: 0.8828 (mt) cc_final: 0.8495 (pp) REVERT: A 134 MET cc_start: 0.7999 (ttp) cc_final: 0.6745 (mpp) REVERT: A 251 ARG cc_start: 0.8947 (mmt90) cc_final: 0.8522 (mmt90) REVERT: A 259 PHE cc_start: 0.6665 (m-80) cc_final: 0.5788 (m-80) REVERT: A 265 TYR cc_start: 0.7435 (m-80) cc_final: 0.7146 (m-80) REVERT: A 280 GLU cc_start: 0.8594 (tt0) cc_final: 0.7992 (tt0) REVERT: G 50 GLU cc_start: 0.8783 (tp30) cc_final: 0.8417 (tp30) REVERT: G 63 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7455 (mmm-85) REVERT: G 67 PHE cc_start: 0.9725 (t80) cc_final: 0.9474 (t80) REVERT: G 73 GLU cc_start: 0.8917 (tt0) cc_final: 0.8187 (tt0) REVERT: G 77 ASP cc_start: 0.9129 (t70) cc_final: 0.8876 (t70) REVERT: G 85 GLN cc_start: 0.9265 (mt0) cc_final: 0.9049 (mt0) REVERT: G 90 MET cc_start: 0.9223 (mmm) cc_final: 0.8937 (mmp) REVERT: G 93 GLN cc_start: 0.9349 (tt0) cc_final: 0.9113 (tt0) REVERT: G 113 HIS cc_start: 0.9080 (t70) cc_final: 0.8615 (t-170) REVERT: H 25 ASN cc_start: 0.8706 (t160) cc_final: 0.8233 (m110) REVERT: H 30 THR cc_start: 0.9342 (p) cc_final: 0.8890 (t) REVERT: H 39 ARG cc_start: 0.8979 (mmt-90) cc_final: 0.8544 (mmp80) REVERT: H 43 VAL cc_start: 0.9523 (t) cc_final: 0.8844 (p) REVERT: H 45 ARG cc_start: 0.8703 (ttt-90) cc_final: 0.8435 (ttt-90) REVERT: H 59 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8647 (ttmm) REVERT: H 68 ASP cc_start: 0.9233 (m-30) cc_final: 0.8877 (m-30) REVERT: H 74 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8649 (tm-30) REVERT: H 92 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8662 (tmm-80) REVERT: I 42 ARG cc_start: 0.9357 (mtm180) cc_final: 0.8992 (ttm110) REVERT: I 57 TYR cc_start: 0.9396 (t80) cc_final: 0.8818 (t80) REVERT: I 61 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8629 (tp30) REVERT: I 75 LYS cc_start: 0.9522 (mmtm) cc_final: 0.9038 (mmtp) REVERT: I 76 THR cc_start: 0.9019 (m) cc_final: 0.8686 (p) REVERT: I 87 VAL cc_start: 0.9530 (m) cc_final: 0.9296 (m) REVERT: I 90 ASP cc_start: 0.8949 (t70) cc_final: 0.8599 (t0) REVERT: I 94 ASN cc_start: 0.8950 (t0) cc_final: 0.8448 (t0) REVERT: I 95 LYS cc_start: 0.9591 (tptt) cc_final: 0.9267 (tppt) REVERT: I 115 LEU cc_start: 0.9322 (mm) cc_final: 0.8973 (mm) REVERT: J 32 GLU cc_start: 0.9179 (pp20) cc_final: 0.8846 (pp20) REVERT: J 44 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8713 (tm-30) REVERT: J 56 MET cc_start: 0.9278 (tpp) cc_final: 0.9050 (tpp) REVERT: J 65 ASP cc_start: 0.8893 (t70) cc_final: 0.8448 (t70) REVERT: J 76 ARG cc_start: 0.9191 (ttm110) cc_final: 0.8906 (ttm110) REVERT: J 81 ASN cc_start: 0.9180 (m-40) cc_final: 0.8046 (p0) REVERT: J 85 THR cc_start: 0.8637 (p) cc_final: 0.8316 (p) REVERT: J 97 LEU cc_start: 0.9334 (mt) cc_final: 0.9129 (mt) REVERT: J 98 LEU cc_start: 0.9073 (tt) cc_final: 0.8868 (tt) REVERT: J 99 LEU cc_start: 0.9211 (mt) cc_final: 0.8885 (mp) REVERT: J 103 LEU cc_start: 0.9282 (mm) cc_final: 0.8737 (mm) REVERT: K 50 GLU cc_start: 0.8356 (tp30) cc_final: 0.7736 (tp30) REVERT: K 52 ARG cc_start: 0.9307 (mtt90) cc_final: 0.8815 (mtm-85) REVERT: K 54 TYR cc_start: 0.8791 (m-10) cc_final: 0.8484 (m-10) REVERT: K 84 PHE cc_start: 0.8937 (m-80) cc_final: 0.8395 (m-10) REVERT: K 85 GLN cc_start: 0.9352 (mm110) cc_final: 0.9132 (mm110) REVERT: K 97 GLU cc_start: 0.9237 (tt0) cc_final: 0.8816 (tt0) REVERT: K 120 MET cc_start: 0.9427 (mmp) cc_final: 0.8957 (mmm) REVERT: K 124 ILE cc_start: 0.9491 (mm) cc_final: 0.9124 (mm) REVERT: K 125 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8673 (mm110) REVERT: M 36 LYS cc_start: 0.9147 (mttm) cc_final: 0.8775 (pttt) REVERT: M 64 GLU cc_start: 0.9455 (tt0) cc_final: 0.8977 (tm-30) REVERT: M 68 ASN cc_start: 0.9541 (m-40) cc_final: 0.8285 (m-40) REVERT: M 102 ILE cc_start: 0.9624 (mm) cc_final: 0.9406 (tp) REVERT: M 112 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8769 (mp10) REVERT: N 43 LYS cc_start: 0.9597 (tppp) cc_final: 0.9357 (tppp) REVERT: N 44 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9056 (tm-30) REVERT: N 65 ASP cc_start: 0.9417 (t0) cc_final: 0.8910 (t0) REVERT: N 83 ARG cc_start: 0.8741 (mmt90) cc_final: 0.8284 (mmm-85) REVERT: N 96 ARG cc_start: 0.8851 (mtp180) cc_final: 0.8519 (ttm110) REVERT: N 105 LYS cc_start: 0.9259 (mttt) cc_final: 0.8858 (mtpt) REVERT: N 110 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8588 (mt-10) REVERT: L 43 VAL cc_start: 0.9706 (t) cc_final: 0.9388 (m) REVERT: L 44 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8387 (mttt) REVERT: L 53 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8071 (tm-30) REVERT: L 63 GLU cc_start: 0.9129 (tp30) cc_final: 0.8725 (tp30) REVERT: L 79 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8031 (mmtm) REVERT: L 88 TYR cc_start: 0.9266 (m-10) cc_final: 0.8801 (m-10) REVERT: L 98 TYR cc_start: 0.8811 (m-80) cc_final: 0.8232 (m-80) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2778 time to fit residues: 140.4162 Evaluate side-chains 307 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN H 25 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN K 108 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15271 Z= 0.314 Angle : 0.641 7.448 21915 Z= 0.371 Chirality : 0.039 0.138 2509 Planarity : 0.005 0.057 1765 Dihedral : 30.069 136.384 4372 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1056 helix: 1.40 (0.21), residues: 544 sheet: -1.68 (0.44), residues: 149 loop : -1.43 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 51 HIS 0.009 0.001 HIS H 75 PHE 0.018 0.002 PHE G 67 TYR 0.054 0.003 TYR H 88 ARG 0.003 0.000 ARG M 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.237 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: A 81 LEU cc_start: 0.8936 (mt) cc_final: 0.8572 (pp) REVERT: A 134 MET cc_start: 0.7942 (ttp) cc_final: 0.6648 (mpp) REVERT: A 242 MET cc_start: 0.7944 (ptp) cc_final: 0.7678 (mpp) REVERT: A 251 ARG cc_start: 0.9029 (mmt90) cc_final: 0.8613 (mmt90) REVERT: A 259 PHE cc_start: 0.6619 (m-80) cc_final: 0.5612 (m-80) REVERT: A 265 TYR cc_start: 0.7531 (m-80) cc_final: 0.7288 (m-80) REVERT: A 280 GLU cc_start: 0.8708 (tt0) cc_final: 0.8271 (tt0) REVERT: G 60 LEU cc_start: 0.9367 (mp) cc_final: 0.9069 (mp) REVERT: G 63 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7424 (mmm-85) REVERT: G 73 GLU cc_start: 0.8900 (tt0) cc_final: 0.8300 (tt0) REVERT: G 77 ASP cc_start: 0.9269 (t70) cc_final: 0.8975 (t70) REVERT: G 85 GLN cc_start: 0.9199 (mt0) cc_final: 0.8684 (mt0) REVERT: G 90 MET cc_start: 0.9221 (mmm) cc_final: 0.9018 (mmm) REVERT: G 93 GLN cc_start: 0.9381 (tt0) cc_final: 0.9150 (tt0) REVERT: G 113 HIS cc_start: 0.9031 (t70) cc_final: 0.8734 (t-170) REVERT: G 125 GLN cc_start: 0.9218 (mt0) cc_final: 0.8778 (mp10) REVERT: H 25 ASN cc_start: 0.8903 (t160) cc_final: 0.8470 (m-40) REVERT: H 30 THR cc_start: 0.9368 (p) cc_final: 0.8930 (t) REVERT: H 43 VAL cc_start: 0.9555 (t) cc_final: 0.9152 (p) REVERT: H 44 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8323 (ttmt) REVERT: H 74 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8670 (tm-30) REVERT: H 75 HIS cc_start: 0.8998 (t-90) cc_final: 0.8692 (t-90) REVERT: H 85 ASP cc_start: 0.9313 (m-30) cc_final: 0.9038 (m-30) REVERT: I 57 TYR cc_start: 0.9423 (t80) cc_final: 0.8850 (t80) REVERT: I 61 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8609 (tp30) REVERT: I 75 LYS cc_start: 0.9570 (mmtm) cc_final: 0.9133 (mmtp) REVERT: I 76 THR cc_start: 0.9042 (m) cc_final: 0.8753 (p) REVERT: I 87 VAL cc_start: 0.9533 (m) cc_final: 0.9106 (m) REVERT: I 90 ASP cc_start: 0.9087 (t70) cc_final: 0.8677 (t0) REVERT: I 94 ASN cc_start: 0.8918 (t0) cc_final: 0.8222 (m-40) REVERT: I 95 LYS cc_start: 0.9609 (tptt) cc_final: 0.9287 (tppt) REVERT: I 115 LEU cc_start: 0.9399 (mm) cc_final: 0.9010 (mm) REVERT: J 32 GLU cc_start: 0.9264 (pp20) cc_final: 0.8918 (pp20) REVERT: J 44 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8786 (tm-30) REVERT: J 56 MET cc_start: 0.9323 (tpp) cc_final: 0.9116 (tpp) REVERT: J 65 ASP cc_start: 0.8872 (t70) cc_final: 0.8412 (t70) REVERT: J 68 GLU cc_start: 0.9211 (tp30) cc_final: 0.8993 (tp30) REVERT: J 81 ASN cc_start: 0.9099 (m-40) cc_final: 0.8025 (p0) REVERT: J 98 LEU cc_start: 0.9211 (tt) cc_final: 0.8892 (tt) REVERT: K 50 GLU cc_start: 0.8823 (tp30) cc_final: 0.8139 (tp30) REVERT: K 52 ARG cc_start: 0.9309 (mtt90) cc_final: 0.8906 (mtm-85) REVERT: K 74 ILE cc_start: 0.9719 (tp) cc_final: 0.9444 (tp) REVERT: K 85 GLN cc_start: 0.9363 (mm110) cc_final: 0.9123 (mm110) REVERT: K 106 ASP cc_start: 0.9188 (m-30) cc_final: 0.8958 (m-30) REVERT: K 120 MET cc_start: 0.9511 (mmp) cc_final: 0.8929 (mmm) REVERT: K 124 ILE cc_start: 0.9533 (mm) cc_final: 0.9255 (mm) REVERT: K 125 GLN cc_start: 0.9340 (mm-40) cc_final: 0.8863 (mm110) REVERT: M 36 LYS cc_start: 0.9163 (mttm) cc_final: 0.8777 (pttt) REVERT: M 56 GLU cc_start: 0.9435 (tt0) cc_final: 0.9192 (mt-10) REVERT: M 64 GLU cc_start: 0.9480 (tt0) cc_final: 0.8971 (tm-30) REVERT: M 68 ASN cc_start: 0.9475 (m-40) cc_final: 0.8109 (m-40) REVERT: M 102 ILE cc_start: 0.9634 (mm) cc_final: 0.9398 (tp) REVERT: M 112 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8836 (mp10) REVERT: N 43 LYS cc_start: 0.9617 (tppp) cc_final: 0.9379 (tppp) REVERT: N 44 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9100 (tm-30) REVERT: N 65 ASP cc_start: 0.9447 (t0) cc_final: 0.8938 (t0) REVERT: N 83 ARG cc_start: 0.8808 (mmt90) cc_final: 0.8344 (mtp85) REVERT: N 85 THR cc_start: 0.9021 (p) cc_final: 0.8684 (p) REVERT: N 96 ARG cc_start: 0.9021 (mtp180) cc_final: 0.8341 (ttm110) REVERT: N 99 LEU cc_start: 0.8879 (mm) cc_final: 0.8143 (tp) REVERT: N 110 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8618 (mt-10) REVERT: L 44 LYS cc_start: 0.9277 (mtpt) cc_final: 0.8602 (mttt) REVERT: L 53 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8115 (tm-30) REVERT: L 63 GLU cc_start: 0.9178 (tp30) cc_final: 0.8711 (tp30) REVERT: L 79 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7931 (mmtm) REVERT: L 98 TYR cc_start: 0.8916 (m-80) cc_final: 0.8252 (m-80) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2673 time to fit residues: 131.6728 Evaluate side-chains 294 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 76 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15271 Z= 0.212 Angle : 0.616 10.143 21915 Z= 0.356 Chirality : 0.038 0.145 2509 Planarity : 0.005 0.085 1765 Dihedral : 29.983 133.671 4372 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 0.23 (0.26), residues: 1056 helix: 1.61 (0.21), residues: 542 sheet: -1.61 (0.44), residues: 149 loop : -1.26 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 51 HIS 0.007 0.001 HIS L 75 PHE 0.018 0.002 PHE K 67 TYR 0.061 0.003 TYR H 88 ARG 0.008 0.000 ARG J 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8934 (mt) cc_final: 0.8557 (pp) REVERT: A 134 MET cc_start: 0.7972 (ttp) cc_final: 0.6677 (mpp) REVERT: A 242 MET cc_start: 0.7945 (ptp) cc_final: 0.7695 (mpp) REVERT: A 251 ARG cc_start: 0.8969 (mmt90) cc_final: 0.8542 (mmt90) REVERT: A 259 PHE cc_start: 0.6685 (m-80) cc_final: 0.5807 (m-80) REVERT: A 265 TYR cc_start: 0.7432 (m-80) cc_final: 0.7151 (m-80) REVERT: A 280 GLU cc_start: 0.8671 (tt0) cc_final: 0.8414 (tt0) REVERT: G 55 GLN cc_start: 0.9453 (mt0) cc_final: 0.9116 (tt0) REVERT: G 63 ARG cc_start: 0.8141 (mmt-90) cc_final: 0.7455 (mmm-85) REVERT: G 67 PHE cc_start: 0.9318 (t80) cc_final: 0.8996 (t80) REVERT: G 73 GLU cc_start: 0.8894 (tt0) cc_final: 0.8236 (tt0) REVERT: G 77 ASP cc_start: 0.9285 (t70) cc_final: 0.9048 (t70) REVERT: G 85 GLN cc_start: 0.9225 (mt0) cc_final: 0.8759 (mt0) REVERT: G 90 MET cc_start: 0.9234 (mmm) cc_final: 0.8960 (mmp) REVERT: G 93 GLN cc_start: 0.9429 (tt0) cc_final: 0.8983 (tm-30) REVERT: G 105 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8598 (tm-30) REVERT: G 109 LEU cc_start: 0.9550 (mm) cc_final: 0.9332 (mp) REVERT: G 125 GLN cc_start: 0.9241 (mt0) cc_final: 0.8759 (mp10) REVERT: H 30 THR cc_start: 0.9324 (p) cc_final: 0.8780 (t) REVERT: H 43 VAL cc_start: 0.9491 (t) cc_final: 0.9128 (p) REVERT: H 44 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8377 (tttt) REVERT: H 63 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8046 (mp0) REVERT: H 74 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8603 (tm-30) REVERT: H 85 ASP cc_start: 0.9319 (m-30) cc_final: 0.9078 (m-30) REVERT: I 42 ARG cc_start: 0.9329 (mtm180) cc_final: 0.8898 (ttm110) REVERT: I 61 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9022 (mm-30) REVERT: I 75 LYS cc_start: 0.9543 (mmtm) cc_final: 0.9109 (mmtp) REVERT: I 76 THR cc_start: 0.8957 (m) cc_final: 0.8685 (p) REVERT: I 87 VAL cc_start: 0.9507 (m) cc_final: 0.9073 (m) REVERT: I 90 ASP cc_start: 0.9061 (t70) cc_final: 0.8609 (t0) REVERT: I 94 ASN cc_start: 0.8832 (t0) cc_final: 0.8122 (m-40) REVERT: I 95 LYS cc_start: 0.9582 (tptt) cc_final: 0.9246 (tppt) REVERT: I 115 LEU cc_start: 0.9324 (mm) cc_final: 0.9025 (mm) REVERT: J 44 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8782 (tm-30) REVERT: J 65 ASP cc_start: 0.8907 (t70) cc_final: 0.8661 (t70) REVERT: J 76 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8778 (ttm110) REVERT: J 81 ASN cc_start: 0.9087 (m-40) cc_final: 0.7916 (p0) REVERT: J 87 THR cc_start: 0.9054 (p) cc_final: 0.8557 (p) REVERT: J 98 LEU cc_start: 0.9203 (tt) cc_final: 0.8878 (tt) REVERT: K 50 GLU cc_start: 0.8893 (tp30) cc_final: 0.8073 (tp30) REVERT: K 52 ARG cc_start: 0.9294 (mtt90) cc_final: 0.8884 (mtm-85) REVERT: K 64 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8962 (mtmm) REVERT: K 74 ILE cc_start: 0.9710 (tp) cc_final: 0.9495 (tp) REVERT: K 84 PHE cc_start: 0.8938 (m-80) cc_final: 0.8429 (m-10) REVERT: K 85 GLN cc_start: 0.9349 (mm110) cc_final: 0.9127 (mm-40) REVERT: K 93 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8937 (tm-30) REVERT: K 106 ASP cc_start: 0.9119 (m-30) cc_final: 0.8894 (m-30) REVERT: K 120 MET cc_start: 0.9520 (mmp) cc_final: 0.8607 (mmm) REVERT: K 125 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8818 (mm110) REVERT: M 36 LYS cc_start: 0.9118 (mttm) cc_final: 0.8752 (pttt) REVERT: M 64 GLU cc_start: 0.9466 (tt0) cc_final: 0.8989 (tm-30) REVERT: M 68 ASN cc_start: 0.9529 (m-40) cc_final: 0.8279 (m-40) REVERT: M 91 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8161 (tm-30) REVERT: M 102 ILE cc_start: 0.9517 (mm) cc_final: 0.9231 (tp) REVERT: N 43 LYS cc_start: 0.9573 (tppp) cc_final: 0.9335 (tppp) REVERT: N 44 GLN cc_start: 0.9425 (tm-30) cc_final: 0.9070 (tm-30) REVERT: N 65 ASP cc_start: 0.9439 (t0) cc_final: 0.8931 (t0) REVERT: N 80 TYR cc_start: 0.8384 (m-80) cc_final: 0.7827 (m-10) REVERT: N 83 ARG cc_start: 0.8629 (mmt90) cc_final: 0.8231 (mmm160) REVERT: N 96 ARG cc_start: 0.8882 (mtp180) cc_final: 0.8564 (ttm110) REVERT: N 105 LYS cc_start: 0.9280 (mttt) cc_final: 0.8946 (mtpt) REVERT: N 110 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8442 (tp30) REVERT: N 113 LYS cc_start: 0.9587 (tmmt) cc_final: 0.9320 (ttpp) REVERT: L 44 LYS cc_start: 0.9387 (mtpt) cc_final: 0.8929 (mttt) REVERT: L 53 GLU cc_start: 0.8508 (tm-30) cc_final: 0.7732 (tm-30) REVERT: L 63 GLU cc_start: 0.9092 (tp30) cc_final: 0.8675 (tp30) REVERT: L 77 LYS cc_start: 0.9423 (mmtp) cc_final: 0.9064 (mmtp) REVERT: L 79 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7697 (mmtm) REVERT: L 88 TYR cc_start: 0.9176 (m-10) cc_final: 0.8221 (m-10) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.2780 time to fit residues: 138.5092 Evaluate side-chains 305 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN G 68 GLN H 25 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15271 Z= 0.311 Angle : 0.655 9.513 21915 Z= 0.376 Chirality : 0.039 0.191 2509 Planarity : 0.005 0.077 1765 Dihedral : 29.998 137.508 4372 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.21 (0.26), residues: 1056 helix: 1.61 (0.22), residues: 534 sheet: -1.61 (0.45), residues: 146 loop : -1.24 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 279 HIS 0.011 0.001 HIS H 75 PHE 0.018 0.002 PHE A 206 TYR 0.029 0.003 TYR N 80 ARG 0.006 0.000 ARG J 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.174 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: A 51 TRP cc_start: 0.7747 (t60) cc_final: 0.7480 (t60) REVERT: A 81 LEU cc_start: 0.8962 (mt) cc_final: 0.8574 (pp) REVERT: A 134 MET cc_start: 0.7955 (ttp) cc_final: 0.6557 (mpp) REVERT: A 242 MET cc_start: 0.7940 (ptp) cc_final: 0.7686 (mpp) REVERT: A 251 ARG cc_start: 0.9052 (mmt90) cc_final: 0.8628 (mmt90) REVERT: A 259 PHE cc_start: 0.6786 (m-80) cc_final: 0.5897 (m-80) REVERT: A 265 TYR cc_start: 0.7450 (m-10) cc_final: 0.7168 (m-80) REVERT: A 280 GLU cc_start: 0.8637 (tt0) cc_final: 0.8137 (tt0) REVERT: A 321 TRP cc_start: 0.6736 (m100) cc_final: 0.6473 (m100) REVERT: G 63 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7530 (mmm-85) REVERT: G 73 GLU cc_start: 0.8841 (tt0) cc_final: 0.8146 (tt0) REVERT: G 77 ASP cc_start: 0.9332 (t70) cc_final: 0.9111 (t70) REVERT: G 90 MET cc_start: 0.9237 (mmm) cc_final: 0.8996 (mmp) REVERT: G 93 GLN cc_start: 0.9479 (tt0) cc_final: 0.9034 (tm-30) REVERT: G 125 GLN cc_start: 0.9273 (mt0) cc_final: 0.8809 (mp10) REVERT: H 25 ASN cc_start: 0.8562 (m-40) cc_final: 0.7704 (m110) REVERT: H 30 THR cc_start: 0.9357 (p) cc_final: 0.8830 (t) REVERT: H 43 VAL cc_start: 0.9567 (t) cc_final: 0.9232 (p) REVERT: H 63 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8101 (mt-10) REVERT: H 74 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8673 (tm-30) REVERT: H 75 HIS cc_start: 0.8957 (t-90) cc_final: 0.8501 (t-90) REVERT: H 85 ASP cc_start: 0.9375 (m-30) cc_final: 0.9129 (m-30) REVERT: I 73 ASN cc_start: 0.9349 (t0) cc_final: 0.9138 (t0) REVERT: I 76 THR cc_start: 0.8937 (m) cc_final: 0.8699 (p) REVERT: I 87 VAL cc_start: 0.9515 (m) cc_final: 0.9231 (m) REVERT: I 90 ASP cc_start: 0.9107 (t70) cc_final: 0.8756 (t0) REVERT: I 94 ASN cc_start: 0.8911 (t0) cc_final: 0.8282 (m-40) REVERT: I 95 LYS cc_start: 0.9595 (tptt) cc_final: 0.9257 (tppt) REVERT: I 115 LEU cc_start: 0.9401 (mm) cc_final: 0.9074 (mm) REVERT: J 44 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8867 (tm-30) REVERT: J 65 ASP cc_start: 0.8954 (t70) cc_final: 0.8698 (t70) REVERT: J 76 ARG cc_start: 0.9065 (ttm110) cc_final: 0.8759 (ttm110) REVERT: J 81 ASN cc_start: 0.8968 (m-40) cc_final: 0.8488 (m-40) REVERT: J 93 THR cc_start: 0.9513 (p) cc_final: 0.9291 (p) REVERT: J 98 LEU cc_start: 0.9169 (tt) cc_final: 0.8849 (tt) REVERT: K 50 GLU cc_start: 0.8949 (tp30) cc_final: 0.8228 (tp30) REVERT: K 52 ARG cc_start: 0.9272 (mtt90) cc_final: 0.8871 (mtm-85) REVERT: K 73 GLU cc_start: 0.8208 (pt0) cc_final: 0.7944 (pt0) REVERT: K 74 ILE cc_start: 0.9743 (tp) cc_final: 0.9484 (tp) REVERT: K 79 LYS cc_start: 0.8256 (tppp) cc_final: 0.7615 (tptm) REVERT: K 97 GLU cc_start: 0.8996 (tt0) cc_final: 0.8780 (tt0) REVERT: K 120 MET cc_start: 0.9317 (mmp) cc_final: 0.8635 (mmm) REVERT: K 123 ASP cc_start: 0.9331 (m-30) cc_final: 0.8384 (m-30) REVERT: K 125 GLN cc_start: 0.9347 (mm-40) cc_final: 0.8864 (mm110) REVERT: M 36 LYS cc_start: 0.9150 (mttm) cc_final: 0.8796 (pttt) REVERT: M 56 GLU cc_start: 0.9451 (tt0) cc_final: 0.9056 (mt-10) REVERT: M 62 ILE cc_start: 0.9663 (mm) cc_final: 0.9299 (tt) REVERT: M 64 GLU cc_start: 0.9435 (tt0) cc_final: 0.8949 (tm-30) REVERT: M 68 ASN cc_start: 0.9462 (m-40) cc_final: 0.8203 (m-40) REVERT: M 102 ILE cc_start: 0.9589 (mm) cc_final: 0.9344 (tp) REVERT: M 112 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8878 (mp10) REVERT: N 43 LYS cc_start: 0.9594 (tppp) cc_final: 0.9342 (tppp) REVERT: N 65 ASP cc_start: 0.9416 (t0) cc_final: 0.8844 (t0) REVERT: N 80 TYR cc_start: 0.8492 (m-80) cc_final: 0.7803 (m-10) REVERT: N 83 ARG cc_start: 0.8709 (mmt90) cc_final: 0.8157 (mtp85) REVERT: N 96 ARG cc_start: 0.9017 (mtp180) cc_final: 0.8358 (ttm110) REVERT: N 110 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8530 (tp30) REVERT: N 113 LYS cc_start: 0.9595 (tmmt) cc_final: 0.9337 (ttpp) REVERT: L 25 ASN cc_start: 0.8050 (t0) cc_final: 0.6909 (t0) REVERT: L 44 LYS cc_start: 0.9365 (mtpt) cc_final: 0.8819 (mttt) REVERT: L 51 TYR cc_start: 0.8890 (m-80) cc_final: 0.8384 (m-80) REVERT: L 53 GLU cc_start: 0.8584 (tm-30) cc_final: 0.7746 (tm-30) REVERT: L 63 GLU cc_start: 0.9143 (tp30) cc_final: 0.8676 (tp30) REVERT: L 77 LYS cc_start: 0.9421 (mmtp) cc_final: 0.9216 (mmtm) REVERT: L 79 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7679 (mmtm) REVERT: L 88 TYR cc_start: 0.9245 (m-10) cc_final: 0.8045 (m-10) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2788 time to fit residues: 131.6552 Evaluate side-chains 290 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS G 68 GLN G 76 GLN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN L 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15271 Z= 0.235 Angle : 0.630 11.583 21915 Z= 0.363 Chirality : 0.038 0.163 2509 Planarity : 0.005 0.070 1765 Dihedral : 29.967 133.472 4372 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.11 % Allowed : 1.01 % Favored : 98.88 % 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: 0.20 (0.26), residues: 1056 helix: 1.66 (0.21), residues: 530 sheet: -1.65 (0.42), residues: 157 loop : -1.28 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 279 HIS 0.009 0.001 HIS H 75 PHE 0.028 0.002 PHE A 206 TYR 0.036 0.003 TYR N 80 ARG 0.007 0.000 ARG I 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.153 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: symmetry clash REVERT: A 51 TRP cc_start: 0.7723 (t60) cc_final: 0.7377 (t60) REVERT: A 81 LEU cc_start: 0.8904 (mt) cc_final: 0.8510 (pp) REVERT: A 134 MET cc_start: 0.7721 (ttp) cc_final: 0.6566 (mpp) REVERT: A 259 PHE cc_start: 0.6799 (m-80) cc_final: 0.6253 (m-80) REVERT: A 265 TYR cc_start: 0.7441 (m-10) cc_final: 0.7214 (m-80) REVERT: A 280 GLU cc_start: 0.8554 (tt0) cc_final: 0.8001 (tt0) REVERT: A 321 TRP cc_start: 0.6722 (m100) cc_final: 0.6480 (m100) REVERT: G 55 GLN cc_start: 0.9450 (mt0) cc_final: 0.9203 (tt0) REVERT: G 63 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7417 (mmm-85) REVERT: G 73 GLU cc_start: 0.8877 (tt0) cc_final: 0.8255 (tt0) REVERT: G 77 ASP cc_start: 0.9319 (t70) cc_final: 0.9110 (t70) REVERT: G 93 GLN cc_start: 0.9435 (tt0) cc_final: 0.9075 (tm-30) REVERT: G 105 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8660 (tm-30) REVERT: H 25 ASN cc_start: 0.8598 (m-40) cc_final: 0.7734 (m110) REVERT: H 30 THR cc_start: 0.9347 (p) cc_final: 0.8802 (t) REVERT: H 43 VAL cc_start: 0.9569 (t) cc_final: 0.9209 (p) REVERT: H 63 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8083 (mt-10) REVERT: H 74 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8794 (tm-30) REVERT: H 75 HIS cc_start: 0.8884 (t-90) cc_final: 0.8262 (t-90) REVERT: H 85 ASP cc_start: 0.9346 (m-30) cc_final: 0.9128 (m-30) REVERT: I 76 THR cc_start: 0.8876 (m) cc_final: 0.8654 (p) REVERT: I 87 VAL cc_start: 0.9472 (m) cc_final: 0.9032 (m) REVERT: I 90 ASP cc_start: 0.9088 (t70) cc_final: 0.8540 (t0) REVERT: I 94 ASN cc_start: 0.8786 (t0) cc_final: 0.8075 (m-40) REVERT: I 95 LYS cc_start: 0.9570 (tptt) cc_final: 0.9220 (tppt) REVERT: I 115 LEU cc_start: 0.9390 (mm) cc_final: 0.9049 (mm) REVERT: J 44 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8864 (tm-30) REVERT: J 65 ASP cc_start: 0.8961 (t70) cc_final: 0.8586 (t70) REVERT: J 81 ASN cc_start: 0.8962 (m-40) cc_final: 0.8519 (m-40) REVERT: J 99 LEU cc_start: 0.9249 (mt) cc_final: 0.9035 (mp) REVERT: K 50 GLU cc_start: 0.8977 (tp30) cc_final: 0.8216 (tp30) REVERT: K 52 ARG cc_start: 0.9252 (mtt90) cc_final: 0.8858 (mtm-85) REVERT: K 64 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8956 (mtmm) REVERT: K 73 GLU cc_start: 0.8230 (pt0) cc_final: 0.7023 (pt0) REVERT: K 74 ILE cc_start: 0.9756 (tp) cc_final: 0.9534 (tp) REVERT: K 79 LYS cc_start: 0.8263 (tppp) cc_final: 0.7617 (tptm) REVERT: K 84 PHE cc_start: 0.9005 (m-10) cc_final: 0.8613 (m-10) REVERT: K 93 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8806 (tm-30) REVERT: K 120 MET cc_start: 0.9277 (mmp) cc_final: 0.8636 (mmm) REVERT: K 123 ASP cc_start: 0.9332 (m-30) cc_final: 0.8531 (m-30) REVERT: M 36 LYS cc_start: 0.9126 (mttm) cc_final: 0.8787 (pttt) REVERT: M 56 GLU cc_start: 0.9421 (tt0) cc_final: 0.9045 (mt-10) REVERT: M 62 ILE cc_start: 0.9624 (mm) cc_final: 0.9144 (tt) REVERT: M 64 GLU cc_start: 0.9429 (tt0) cc_final: 0.8935 (tm-30) REVERT: M 68 ASN cc_start: 0.9501 (m-40) cc_final: 0.8323 (m-40) REVERT: M 102 ILE cc_start: 0.9543 (mm) cc_final: 0.9248 (tp) REVERT: N 43 LYS cc_start: 0.9586 (tppp) cc_final: 0.9341 (tppp) REVERT: N 65 ASP cc_start: 0.9407 (t0) cc_final: 0.8881 (t0) REVERT: N 76 ARG cc_start: 0.9536 (ttm-80) cc_final: 0.9046 (ttm-80) REVERT: N 80 TYR cc_start: 0.8592 (m-80) cc_final: 0.8221 (m-10) REVERT: N 83 ARG cc_start: 0.8735 (mmt90) cc_final: 0.8334 (mmm-85) REVERT: N 96 ARG cc_start: 0.8960 (mtp180) cc_final: 0.8340 (ttm110) REVERT: N 105 LYS cc_start: 0.9157 (mttt) cc_final: 0.8862 (mtpt) REVERT: N 110 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8514 (tp30) REVERT: N 113 LYS cc_start: 0.9571 (tmmt) cc_final: 0.9315 (ttpp) REVERT: L 25 ASN cc_start: 0.8163 (t0) cc_final: 0.7272 (m110) REVERT: L 44 LYS cc_start: 0.9339 (mtpt) cc_final: 0.8820 (mttt) REVERT: L 51 TYR cc_start: 0.8788 (m-80) cc_final: 0.8408 (m-80) REVERT: L 63 GLU cc_start: 0.9100 (tp30) cc_final: 0.8692 (tp30) REVERT: L 79 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7551 (mmtm) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.2729 time to fit residues: 131.1755 Evaluate side-chains 298 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS G 68 GLN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN K 108 ASN L 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15271 Z= 0.208 Angle : 0.627 10.431 21915 Z= 0.359 Chirality : 0.038 0.155 2509 Planarity : 0.005 0.065 1765 Dihedral : 29.873 134.081 4372 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.11 % Allowed : 0.89 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1056 helix: 1.65 (0.22), residues: 530 sheet: -1.52 (0.43), residues: 157 loop : -1.28 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 279 HIS 0.009 0.001 HIS H 75 PHE 0.022 0.002 PHE A 206 TYR 0.045 0.003 TYR L 88 ARG 0.007 0.000 ARG I 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 1.210 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TRP cc_start: 0.7750 (t60) cc_final: 0.7383 (t60) REVERT: A 81 LEU cc_start: 0.8838 (mt) cc_final: 0.8462 (pp) REVERT: A 134 MET cc_start: 0.7815 (ttp) cc_final: 0.6703 (mpp) REVERT: A 167 TYR cc_start: 0.7300 (m-10) cc_final: 0.6887 (m-80) REVERT: A 242 MET cc_start: 0.7954 (ptp) cc_final: 0.7609 (mpp) REVERT: A 280 GLU cc_start: 0.8600 (tt0) cc_final: 0.7949 (tt0) REVERT: A 321 TRP cc_start: 0.6910 (m100) cc_final: 0.6677 (m100) REVERT: G 55 GLN cc_start: 0.9460 (mt0) cc_final: 0.9148 (tt0) REVERT: G 63 ARG cc_start: 0.8092 (mmt-90) cc_final: 0.7443 (mmm-85) REVERT: G 73 GLU cc_start: 0.8888 (tt0) cc_final: 0.8550 (tt0) REVERT: G 93 GLN cc_start: 0.9413 (tt0) cc_final: 0.9092 (tm-30) REVERT: G 105 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8684 (tm-30) REVERT: G 125 GLN cc_start: 0.9089 (mt0) cc_final: 0.8799 (mp10) REVERT: H 25 ASN cc_start: 0.8621 (m-40) cc_final: 0.7958 (m110) REVERT: H 30 THR cc_start: 0.9260 (p) cc_final: 0.8687 (t) REVERT: H 31 LYS cc_start: 0.9273 (tmtt) cc_final: 0.9063 (tptp) REVERT: H 50 ILE cc_start: 0.9559 (mm) cc_final: 0.9286 (mm) REVERT: H 52 GLU cc_start: 0.8854 (pm20) cc_final: 0.7869 (pp20) REVERT: H 53 GLU cc_start: 0.8645 (tt0) cc_final: 0.8259 (tt0) REVERT: H 63 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8083 (mt-10) REVERT: H 71 THR cc_start: 0.9777 (m) cc_final: 0.9439 (p) REVERT: H 74 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8734 (tm-30) REVERT: H 75 HIS cc_start: 0.8833 (t-90) cc_final: 0.8264 (t-90) REVERT: H 84 MET cc_start: 0.9167 (mmm) cc_final: 0.8603 (mmm) REVERT: H 88 TYR cc_start: 0.8995 (m-80) cc_final: 0.8246 (m-80) REVERT: I 76 THR cc_start: 0.8819 (m) cc_final: 0.8614 (p) REVERT: I 87 VAL cc_start: 0.9432 (m) cc_final: 0.9012 (m) REVERT: I 90 ASP cc_start: 0.9010 (t70) cc_final: 0.8468 (t0) REVERT: I 94 ASN cc_start: 0.8670 (t0) cc_final: 0.7974 (m-40) REVERT: I 95 LYS cc_start: 0.9506 (tptt) cc_final: 0.9262 (ttmm) REVERT: I 115 LEU cc_start: 0.9355 (mm) cc_final: 0.9087 (mm) REVERT: J 44 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8816 (tm-30) REVERT: J 65 ASP cc_start: 0.8913 (t70) cc_final: 0.8629 (t70) REVERT: J 81 ASN cc_start: 0.8986 (m-40) cc_final: 0.8557 (m-40) REVERT: J 97 LEU cc_start: 0.9260 (mt) cc_final: 0.9035 (mt) REVERT: J 99 LEU cc_start: 0.9143 (mt) cc_final: 0.8880 (mp) REVERT: K 50 GLU cc_start: 0.8951 (tp30) cc_final: 0.8142 (tp30) REVERT: K 52 ARG cc_start: 0.9238 (mtt90) cc_final: 0.8734 (mtm-85) REVERT: K 56 LYS cc_start: 0.9499 (tptp) cc_final: 0.9241 (tppp) REVERT: K 64 LYS cc_start: 0.9145 (mtmt) cc_final: 0.8907 (mtmm) REVERT: K 73 GLU cc_start: 0.8377 (pt0) cc_final: 0.7238 (pt0) REVERT: K 79 LYS cc_start: 0.8268 (tppp) cc_final: 0.7596 (tptm) REVERT: K 84 PHE cc_start: 0.9058 (m-10) cc_final: 0.8782 (m-10) REVERT: K 120 MET cc_start: 0.9243 (mmp) cc_final: 0.8663 (mmm) REVERT: K 123 ASP cc_start: 0.9264 (m-30) cc_final: 0.8522 (m-30) REVERT: M 36 LYS cc_start: 0.9109 (mttm) cc_final: 0.8731 (pttt) REVERT: M 56 GLU cc_start: 0.9436 (tt0) cc_final: 0.9053 (mt-10) REVERT: M 62 ILE cc_start: 0.9608 (mm) cc_final: 0.9128 (tt) REVERT: M 64 GLU cc_start: 0.9409 (tt0) cc_final: 0.8969 (tm-30) REVERT: M 68 ASN cc_start: 0.9544 (m-40) cc_final: 0.8377 (m-40) REVERT: M 102 ILE cc_start: 0.9455 (mm) cc_final: 0.9189 (tp) REVERT: N 65 ASP cc_start: 0.9430 (t0) cc_final: 0.8941 (t0) REVERT: N 68 GLU cc_start: 0.8798 (tp30) cc_final: 0.8516 (tp30) REVERT: N 80 TYR cc_start: 0.8458 (m-80) cc_final: 0.7820 (m-80) REVERT: N 83 ARG cc_start: 0.8678 (mmt90) cc_final: 0.8307 (mmm160) REVERT: N 96 ARG cc_start: 0.8936 (mtp180) cc_final: 0.8308 (ttm110) REVERT: N 110 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8556 (tp30) REVERT: N 113 LYS cc_start: 0.9560 (tmmt) cc_final: 0.9273 (ttpp) REVERT: L 25 ASN cc_start: 0.8041 (t0) cc_final: 0.7279 (m110) REVERT: L 44 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8813 (mttt) REVERT: L 63 GLU cc_start: 0.9027 (tp30) cc_final: 0.8583 (tp30) REVERT: L 79 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7451 (mmtm) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.2749 time to fit residues: 132.7300 Evaluate side-chains 301 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.0470 chunk 59 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS G 68 GLN G 76 GLN I 38 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15271 Z= 0.228 Angle : 0.630 11.140 21915 Z= 0.360 Chirality : 0.038 0.176 2509 Planarity : 0.005 0.065 1765 Dihedral : 29.826 134.222 4372 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1056 helix: 1.62 (0.22), residues: 536 sheet: -1.34 (0.44), residues: 157 loop : -1.29 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 74 HIS 0.008 0.001 HIS H 75 PHE 0.031 0.002 PHE A 206 TYR 0.048 0.003 TYR H 88 ARG 0.007 0.000 ARG J 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.324 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: A 51 TRP cc_start: 0.7771 (t60) cc_final: 0.7424 (t60) REVERT: A 81 LEU cc_start: 0.8803 (mt) cc_final: 0.8398 (pp) REVERT: A 134 MET cc_start: 0.7818 (ttp) cc_final: 0.6688 (mpp) REVERT: A 242 MET cc_start: 0.7985 (ptp) cc_final: 0.7634 (mpp) REVERT: A 251 ARG cc_start: 0.8761 (mmt-90) cc_final: 0.8395 (mmt-90) REVERT: A 280 GLU cc_start: 0.8579 (tt0) cc_final: 0.8115 (tt0) REVERT: A 321 TRP cc_start: 0.6879 (m100) cc_final: 0.6607 (m100) REVERT: G 63 ARG cc_start: 0.8067 (mmt-90) cc_final: 0.7665 (mmm-85) REVERT: G 73 GLU cc_start: 0.8907 (tt0) cc_final: 0.8591 (tt0) REVERT: G 93 GLN cc_start: 0.9374 (tt0) cc_final: 0.8921 (tm-30) REVERT: G 125 GLN cc_start: 0.9046 (mt0) cc_final: 0.8760 (mp10) REVERT: H 25 ASN cc_start: 0.8603 (m-40) cc_final: 0.7971 (m110) REVERT: H 30 THR cc_start: 0.9266 (p) cc_final: 0.8667 (t) REVERT: H 50 ILE cc_start: 0.9543 (mm) cc_final: 0.9245 (mm) REVERT: H 52 GLU cc_start: 0.8837 (pm20) cc_final: 0.7836 (pp20) REVERT: H 53 GLU cc_start: 0.8707 (tt0) cc_final: 0.8314 (tt0) REVERT: H 63 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8054 (mt-10) REVERT: H 71 THR cc_start: 0.9767 (m) cc_final: 0.9422 (p) REVERT: H 74 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8716 (tm-30) REVERT: H 75 HIS cc_start: 0.8823 (t-90) cc_final: 0.8268 (t-90) REVERT: H 84 MET cc_start: 0.9242 (mmm) cc_final: 0.8656 (mmm) REVERT: I 61 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8867 (mm-30) REVERT: I 73 ASN cc_start: 0.9312 (t0) cc_final: 0.8973 (t0) REVERT: I 75 LYS cc_start: 0.9548 (mmtm) cc_final: 0.8997 (mmtp) REVERT: I 87 VAL cc_start: 0.9413 (m) cc_final: 0.8996 (m) REVERT: I 90 ASP cc_start: 0.9010 (t70) cc_final: 0.8517 (t0) REVERT: I 94 ASN cc_start: 0.8734 (t0) cc_final: 0.8092 (m-40) REVERT: I 95 LYS cc_start: 0.9507 (tptt) cc_final: 0.9277 (ttmm) REVERT: I 115 LEU cc_start: 0.9386 (mm) cc_final: 0.9048 (mm) REVERT: J 44 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8840 (tm-30) REVERT: J 65 ASP cc_start: 0.8894 (t70) cc_final: 0.8613 (t70) REVERT: J 73 GLU cc_start: 0.9428 (tp30) cc_final: 0.9228 (mm-30) REVERT: J 76 ARG cc_start: 0.9156 (ttm110) cc_final: 0.8888 (ttm110) REVERT: J 81 ASN cc_start: 0.8988 (m-40) cc_final: 0.8637 (m-40) REVERT: J 99 LEU cc_start: 0.9161 (mt) cc_final: 0.8890 (mp) REVERT: K 50 GLU cc_start: 0.8979 (tp30) cc_final: 0.8208 (tp30) REVERT: K 52 ARG cc_start: 0.9218 (mtt90) cc_final: 0.8709 (mtm-85) REVERT: K 56 LYS cc_start: 0.9481 (tptp) cc_final: 0.9242 (tppp) REVERT: K 64 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8891 (mtmm) REVERT: K 73 GLU cc_start: 0.8410 (pt0) cc_final: 0.7369 (pt0) REVERT: K 79 LYS cc_start: 0.8261 (tppp) cc_final: 0.7589 (tptm) REVERT: K 84 PHE cc_start: 0.9113 (m-10) cc_final: 0.8840 (m-10) REVERT: K 90 MET cc_start: 0.9155 (mtm) cc_final: 0.8780 (mtt) REVERT: K 93 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8689 (tm-30) REVERT: K 120 MET cc_start: 0.9229 (mmp) cc_final: 0.8595 (mmm) REVERT: K 123 ASP cc_start: 0.9275 (m-30) cc_final: 0.8539 (m-30) REVERT: M 36 LYS cc_start: 0.9109 (mttm) cc_final: 0.8735 (pttt) REVERT: M 56 GLU cc_start: 0.9395 (tt0) cc_final: 0.9020 (mt-10) REVERT: M 64 GLU cc_start: 0.9421 (tt0) cc_final: 0.8975 (tm-30) REVERT: M 68 ASN cc_start: 0.9531 (m-40) cc_final: 0.8395 (m-40) REVERT: M 102 ILE cc_start: 0.9476 (mm) cc_final: 0.9214 (tp) REVERT: N 65 ASP cc_start: 0.9428 (t0) cc_final: 0.8961 (t0) REVERT: N 68 GLU cc_start: 0.8824 (tp30) cc_final: 0.8560 (tp30) REVERT: N 80 TYR cc_start: 0.8222 (m-80) cc_final: 0.7085 (m-10) REVERT: N 83 ARG cc_start: 0.8671 (mmt90) cc_final: 0.8201 (mmm160) REVERT: N 96 ARG cc_start: 0.8964 (mtp180) cc_final: 0.8331 (ttm110) REVERT: N 102 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8476 (mm-30) REVERT: N 105 LYS cc_start: 0.9108 (mttt) cc_final: 0.8615 (mtpp) REVERT: N 110 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8549 (tp30) REVERT: N 113 LYS cc_start: 0.9489 (tmmt) cc_final: 0.9266 (ttpp) REVERT: L 25 ASN cc_start: 0.8029 (t0) cc_final: 0.7241 (m110) REVERT: L 44 LYS cc_start: 0.9318 (mtpt) cc_final: 0.8668 (mttt) REVERT: L 63 GLU cc_start: 0.9035 (tp30) cc_final: 0.8609 (tp30) REVERT: L 88 TYR cc_start: 0.9067 (m-10) cc_final: 0.8233 (m-10) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2666 time to fit residues: 128.7330 Evaluate side-chains 297 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN H 64 ASN I 38 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.039224 restraints weight = 81439.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.040625 restraints weight = 38530.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.041551 restraints weight = 24013.842| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 15271 Z= 0.448 Angle : 0.746 9.574 21915 Z= 0.423 Chirality : 0.042 0.159 2509 Planarity : 0.006 0.065 1765 Dihedral : 30.142 142.450 4372 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.06 (0.26), residues: 1056 helix: 1.32 (0.22), residues: 530 sheet: -1.55 (0.44), residues: 151 loop : -1.32 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 74 HIS 0.011 0.002 HIS H 75 PHE 0.025 0.003 PHE A 206 TYR 0.052 0.004 TYR H 88 ARG 0.007 0.001 ARG I 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.88 seconds wall clock time: 57 minutes 8.03 seconds (3428.03 seconds total)