Starting phenix.real_space_refine on Sat Nov 16 18:28:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/11_2024/8euj_28614_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/11_2024/8euj_28614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/11_2024/8euj_28614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/11_2024/8euj_28614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/11_2024/8euj_28614_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euj_28614/11_2024/8euj_28614_neut.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 12 5.16 5 C 6591 2.51 5 N 2205 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11913 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 765 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "b" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "f" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 782 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU O 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU O 22 " occ=0.00 residue: pdb=" N ARG O 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG O 23 " occ=0.00 Time building chain proxies: 10.69, per 1000 atoms: 0.90 Number of scatterers: 11913 At special positions: 0 Unit cell: (116.065, 120.24, 104.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 292 15.00 O 2813 8.00 N 2205 7.00 C 6591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 886.3 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 73.0% alpha, 1.6% beta 147 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.503A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.765A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.520A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.545A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.555A pdb=" N ALA M 114 " --> pdb=" O CYS M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.779A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 29 removed outlier: 4.088A pdb=" N ILE O 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 41 Processing helix chain 'O' and resid 50 through 76 removed outlier: 4.044A pdb=" N ASP O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 93 removed outlier: 3.745A pdb=" N VAL O 86 " --> pdb=" O THR O 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 22 Processing helix chain 'a' and resid 26 through 37 Processing helix chain 'a' and resid 45 through 72 removed outlier: 4.141A pdb=" N VAL a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 89 removed outlier: 3.666A pdb=" N ASN a 89 " --> pdb=" O LEU a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 97 Processing helix chain 'b' and resid 34 through 46 removed outlier: 4.186A pdb=" N VAL b 38 " --> pdb=" O TYR b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 80 Processing helix chain 'b' and resid 87 through 99 removed outlier: 3.759A pdb=" N LEU b 98 " --> pdb=" O ALA b 94 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU b 99 " --> pdb=" O VAL b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 121 removed outlier: 3.884A pdb=" N ALA b 121 " --> pdb=" O LYS b 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 57 Processing helix chain 'f' and resid 63 through 79 removed outlier: 3.955A pdb=" N PHE f 67 " --> pdb=" O ARG f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 114 Processing helix chain 'f' and resid 121 through 131 Processing helix chain 'h' and resid 24 through 29 removed outlier: 3.529A pdb=" N GLN h 27 " --> pdb=" O ASP h 24 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE h 29 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 42 Processing helix chain 'h' and resid 49 through 76 removed outlier: 3.612A pdb=" N ALA h 76 " --> pdb=" O TYR h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 94 removed outlier: 3.823A pdb=" N VAL h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 22 removed outlier: 3.776A pdb=" N ARG k 20 " --> pdb=" O THR k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 36 removed outlier: 3.995A pdb=" N VAL k 30 " --> pdb=" O PRO k 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 74 removed outlier: 4.404A pdb=" N VAL k 49 " --> pdb=" O ALA k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 79 through 88 Processing helix chain 'k' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'H' and resid 50 through 51 removed outlier: 7.857A pdb=" N GLY H 50 " --> pdb=" O ILE k 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG M 83 " --> pdb=" O VAL O 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 96 through 97 removed outlier: 6.869A pdb=" N THR O 96 " --> pdb=" O THR k 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'f' and resid 83 through 84 removed outlier: 7.148A pdb=" N ARG f 83 " --> pdb=" O VAL h 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 390 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2637 1.34 - 1.46: 4499 1.46 - 1.58: 4978 1.58 - 1.71: 585 1.71 - 1.83: 22 Bond restraints: 12721 Sorted by residual: bond pdb=" C ILE a 79 " pdb=" N PRO a 80 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.08e-02 8.57e+03 9.40e+00 bond pdb=" CB PRO a 109 " pdb=" CG PRO a 109 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.96e+00 bond pdb=" CB ASN k 73 " pdb=" CG ASN k 73 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.15e+00 bond pdb=" CB ASN H 60 " pdb=" CG ASN H 60 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.91e+00 bond pdb=" CB ASN a 38 " pdb=" CG ASN a 38 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.76e+00 ... (remaining 12716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 18248 4.68 - 9.36: 170 9.36 - 14.05: 26 14.05 - 18.73: 3 18.73 - 23.41: 1 Bond angle restraints: 18448 Sorted by residual: angle pdb=" CA PRO a 109 " pdb=" N PRO a 109 " pdb=" CD PRO a 109 " ideal model delta sigma weight residual 112.00 99.08 12.92 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA LEU f 65 " pdb=" CB LEU f 65 " pdb=" CG LEU f 65 " ideal model delta sigma weight residual 116.30 139.71 -23.41 3.50e+00 8.16e-02 4.47e+01 angle pdb=" CA PRO f 43 " pdb=" N PRO f 43 " pdb=" CD PRO f 43 " ideal model delta sigma weight residual 112.00 103.70 8.30 1.40e+00 5.10e-01 3.51e+01 angle pdb=" CA LYS M 64 " pdb=" CB LYS M 64 " pdb=" CG LYS M 64 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.51e+01 angle pdb=" CA ARG b 89 " pdb=" CB ARG b 89 " pdb=" CG ARG b 89 " ideal model delta sigma weight residual 114.10 125.01 -10.91 2.00e+00 2.50e-01 2.98e+01 ... (remaining 18443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3951 18.00 - 36.00: 1366 36.00 - 54.00: 1251 54.00 - 72.00: 355 72.00 - 90.00: 52 Dihedral angle restraints: 6975 sinusoidal: 4809 harmonic: 2166 Sorted by residual: dihedral pdb=" CA ILE O 50 " pdb=" C ILE O 50 " pdb=" N TYR O 51 " pdb=" CA TYR O 51 " ideal model delta harmonic sigma weight residual 180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU b 97 " pdb=" C LEU b 97 " pdb=" N LEU b 98 " pdb=" CA LEU b 98 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU a 108 " pdb=" C LEU a 108 " pdb=" N PRO a 109 " pdb=" CA PRO a 109 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1866 0.083 - 0.167: 213 0.167 - 0.250: 17 0.250 - 0.334: 4 0.334 - 0.417: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CB VAL H 108 " pdb=" CA VAL H 108 " pdb=" CG1 VAL H 108 " pdb=" CG2 VAL H 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB ILE H 58 " pdb=" CA ILE H 58 " pdb=" CG1 ILE H 58 " pdb=" CG2 ILE H 58 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CB VAL H 41 " pdb=" CA VAL H 41 " pdb=" CG1 VAL H 41 " pdb=" CG2 VAL H 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2101 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a 108 " -0.106 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO a 109 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO a 109 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO a 109 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG f 42 " 0.069 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO f 43 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO f 43 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO f 43 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR h 88 " 0.026 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR h 88 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR h 88 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR h 88 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR h 88 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR h 88 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR h 88 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR h 88 " -0.002 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1827 2.77 - 3.30: 10431 3.30 - 3.83: 25130 3.83 - 4.37: 27389 4.37 - 4.90: 37898 Nonbonded interactions: 102675 Sorted by model distance: nonbonded pdb=" O LEU a 55 " pdb=" OG1 THR a 59 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP b 65 " pdb=" OH TYR h 98 " model vdw 2.259 3.040 nonbonded pdb=" OP1 DT J 18 " pdb=" NZ LYS M 64 " model vdw 2.267 3.120 nonbonded pdb=" O TYR a 39 " pdb=" OG SER b 75 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP H 65 " pdb=" OH TYR O 98 " model vdw 2.294 3.040 ... (remaining 102670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'H' and resid 30 through 121) selection = (chain 'b' and (resid 30 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 121)) } ncs_group { reference = (chain 'I' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'J' and (resid -73 through -1 or resid 1 through 73)) } ncs_group { reference = (chain 'M' and (resid 41 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 135)) selection = (chain 'f' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 133 or (resid 134 and (name N or n \ ame CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'O' and (resid 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 102)) selection = chain 'h' } ncs_group { reference = (chain 'a' and resid 15 through 118) selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.110 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.300 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 12721 Z= 0.349 Angle : 1.221 23.411 18448 Z= 0.645 Chirality : 0.057 0.417 2104 Planarity : 0.011 0.150 1319 Dihedral : 30.772 89.997 5577 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 40.55 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.27), residues: 730 helix: -1.65 (0.19), residues: 517 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS O 75 PHE 0.056 0.004 PHE O 61 TYR 0.065 0.005 TYR h 88 ARG 0.024 0.002 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7442 (mm-30) REVERT: a 112 GLN cc_start: 0.6722 (tp-100) cc_final: 0.6424 (tm-30) REVERT: b 73 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7758 (mm-30) REVERT: b 76 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8527 (ttm110) REVERT: f 90 MET cc_start: 0.8427 (mmm) cc_final: 0.8214 (mmm) REVERT: k 35 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8339 (mpp80) REVERT: k 71 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8224 (mtt90) REVERT: k 91 GLU cc_start: 0.8103 (pp20) cc_final: 0.7599 (pp20) REVERT: k 92 GLU cc_start: 0.7888 (pm20) cc_final: 0.7657 (pm20) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3160 time to fit residues: 113.6123 Evaluate side-chains 258 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.0270 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN M 125 GLN ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN b 79 HIS k 82 HIS k 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12721 Z= 0.207 Angle : 0.723 16.735 18448 Z= 0.411 Chirality : 0.037 0.199 2104 Planarity : 0.006 0.074 1319 Dihedral : 32.232 89.771 4127 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.72 % Allowed : 33.06 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.28), residues: 730 helix: -0.19 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -1.52 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS O 75 PHE 0.013 0.001 PHE H 67 TYR 0.036 0.002 TYR O 88 ARG 0.012 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.991 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: H 39 TYR cc_start: 0.7767 (t80) cc_final: 0.7426 (t80) REVERT: H 40 LYS cc_start: 0.9043 (pttm) cc_final: 0.8597 (ptpp) REVERT: M 131 ARG cc_start: 0.7937 (ptm160) cc_final: 0.7712 (ptp-170) REVERT: b 30 ARG cc_start: 0.6640 (mmm160) cc_final: 0.5409 (mmp80) REVERT: b 76 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8550 (ttm110) REVERT: k 35 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8350 (mpp80) REVERT: k 91 GLU cc_start: 0.8141 (pp20) cc_final: 0.7761 (pp20) outliers start: 29 outliers final: 22 residues processed: 265 average time/residue: 0.3162 time to fit residues: 110.5759 Evaluate side-chains 252 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 57 SER Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 38 ASN a 112 GLN b 79 HIS k 24 GLN k 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12721 Z= 0.329 Angle : 0.772 13.841 18448 Z= 0.442 Chirality : 0.040 0.154 2104 Planarity : 0.007 0.061 1319 Dihedral : 32.587 89.587 4127 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 9.45 % Allowed : 29.64 % Favored : 60.91 % 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: -0.53 (0.29), residues: 730 helix: 0.16 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.002 HIS b 79 PHE 0.014 0.002 PHE k 25 TYR 0.039 0.003 TYR O 88 ARG 0.009 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8855 (tptt) cc_final: 0.8573 (tppt) REVERT: H 102 GLU cc_start: 0.8545 (pm20) cc_final: 0.8051 (pp20) REVERT: M 105 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7700 (mm-30) REVERT: M 131 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7701 (ptm-80) REVERT: O 88 TYR cc_start: 0.7763 (m-80) cc_final: 0.7552 (m-80) REVERT: a 65 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8293 (mm) REVERT: b 64 ASN cc_start: 0.8811 (m-40) cc_final: 0.8606 (m-40) REVERT: b 76 ARG cc_start: 0.8842 (ttm110) cc_final: 0.8531 (ttm110) REVERT: b 113 LYS cc_start: 0.7921 (pptt) cc_final: 0.7681 (pptt) REVERT: f 77 ASP cc_start: 0.8488 (m-30) cc_final: 0.8171 (m-30) REVERT: f 83 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7803 (mmm160) REVERT: k 23 LEU cc_start: 0.7678 (mt) cc_final: 0.7292 (mp) REVERT: k 35 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8392 (mpp80) REVERT: k 61 GLU cc_start: 0.8088 (tp30) cc_final: 0.7835 (tp30) REVERT: k 92 GLU cc_start: 0.8018 (pm20) cc_final: 0.7654 (pm20) outliers start: 58 outliers final: 40 residues processed: 268 average time/residue: 0.2913 time to fit residues: 104.4124 Evaluate side-chains 267 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain a residue 114 VAL Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 83 ARG Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 GLN k 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12721 Z= 0.214 Angle : 0.712 12.665 18448 Z= 0.407 Chirality : 0.037 0.152 2104 Planarity : 0.005 0.059 1319 Dihedral : 32.277 87.597 4127 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.86 % Allowed : 32.90 % Favored : 61.24 % 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: -0.04 (0.30), residues: 730 helix: 0.61 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.60 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS O 75 PHE 0.014 0.001 PHE b 62 TYR 0.038 0.002 TYR O 88 ARG 0.009 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.8864 (tptt) cc_final: 0.8516 (tppt) REVERT: H 32 GLU cc_start: 0.8138 (pp20) cc_final: 0.7746 (pp20) REVERT: H 102 GLU cc_start: 0.8499 (pm20) cc_final: 0.8079 (pp20) REVERT: M 105 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7571 (mm-30) REVERT: M 131 ARG cc_start: 0.8098 (ptm160) cc_final: 0.7668 (ptm-80) REVERT: a 33 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8983 (mm) REVERT: a 42 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7586 (ttp80) REVERT: a 65 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8260 (mm) REVERT: f 90 MET cc_start: 0.8428 (mmp) cc_final: 0.8141 (mmm) REVERT: h 35 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8162 (mtp-110) REVERT: k 23 LEU cc_start: 0.7568 (mt) cc_final: 0.7211 (mp) REVERT: k 24 GLN cc_start: 0.7232 (tp40) cc_final: 0.6833 (tt0) REVERT: k 35 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8382 (mpp80) outliers start: 36 outliers final: 24 residues processed: 272 average time/residue: 0.2737 time to fit residues: 99.9927 Evaluate side-chains 261 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN a 112 GLN b 79 HIS k 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12721 Z= 0.198 Angle : 0.719 14.950 18448 Z= 0.404 Chirality : 0.037 0.174 2104 Planarity : 0.005 0.058 1319 Dihedral : 32.082 88.006 4127 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.19 % Allowed : 33.55 % Favored : 60.26 % 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: 0.32 (0.30), residues: 730 helix: 0.88 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS O 75 PHE 0.014 0.001 PHE b 62 TYR 0.031 0.002 TYR H 80 ARG 0.010 0.001 ARG b 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 56 MET cc_start: 0.8509 (tmm) cc_final: 0.8277 (ppp) REVERT: H 102 GLU cc_start: 0.8464 (pm20) cc_final: 0.8049 (pp20) REVERT: M 105 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7657 (mm-30) REVERT: M 131 ARG cc_start: 0.8124 (ptm160) cc_final: 0.7211 (ptm-80) REVERT: a 33 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8968 (mm) REVERT: a 42 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7684 (ttp80) REVERT: a 65 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8202 (mm) REVERT: a 95 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8858 (mtpp) REVERT: b 64 ASN cc_start: 0.8539 (m-40) cc_final: 0.8296 (m110) REVERT: h 27 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7468 (tp-100) REVERT: h 66 ILE cc_start: 0.8990 (pt) cc_final: 0.8580 (mt) REVERT: k 35 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8409 (mpp80) outliers start: 38 outliers final: 23 residues processed: 276 average time/residue: 0.3072 time to fit residues: 112.4408 Evaluate side-chains 264 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 60 LEU Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 38 ASN Chi-restraints excluded: chain k residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12721 Z= 0.241 Angle : 0.735 13.830 18448 Z= 0.417 Chirality : 0.038 0.178 2104 Planarity : 0.006 0.063 1319 Dihedral : 32.118 87.967 4127 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.68 % Allowed : 34.20 % Favored : 59.12 % 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: 0.29 (0.30), residues: 730 helix: 0.85 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS b 79 PHE 0.020 0.002 PHE O 61 TYR 0.032 0.002 TYR H 80 ARG 0.012 0.001 ARG k 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 GLU cc_start: 0.8146 (pp20) cc_final: 0.7743 (pp20) REVERT: H 40 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8862 (ptpp) REVERT: H 98 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8052 (tt) REVERT: H 102 GLU cc_start: 0.8483 (pm20) cc_final: 0.8105 (pp20) REVERT: M 105 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7697 (mm-30) REVERT: M 131 ARG cc_start: 0.8222 (ptm160) cc_final: 0.8008 (ptm-80) REVERT: a 33 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8982 (mm) REVERT: a 42 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7716 (ttp80) REVERT: a 65 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8258 (mm) REVERT: h 66 ILE cc_start: 0.9061 (pt) cc_final: 0.8529 (mt) REVERT: k 23 LEU cc_start: 0.7661 (mt) cc_final: 0.7243 (mp) REVERT: k 35 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8417 (mpp80) outliers start: 41 outliers final: 30 residues processed: 261 average time/residue: 0.3000 time to fit residues: 104.1478 Evaluate side-chains 267 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 101 THR Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 71 THR Chi-restraints excluded: chain h residue 85 ASP Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12721 Z= 0.207 Angle : 0.745 13.524 18448 Z= 0.416 Chirality : 0.038 0.227 2104 Planarity : 0.005 0.062 1319 Dihedral : 32.036 88.977 4127 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.35 % Allowed : 35.67 % Favored : 57.98 % 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: 0.29 (0.30), residues: 730 helix: 0.85 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.49 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.002 HIS b 79 PHE 0.016 0.002 PHE b 62 TYR 0.034 0.002 TYR H 80 ARG 0.009 0.001 ARG b 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 40 LYS cc_start: 0.9096 (ptpp) cc_final: 0.8555 (ptpp) REVERT: H 98 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8056 (tt) REVERT: H 102 GLU cc_start: 0.8465 (pm20) cc_final: 0.8108 (pp20) REVERT: M 105 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7725 (mm-30) REVERT: M 133 GLU cc_start: 0.7561 (mp0) cc_final: 0.6855 (pm20) REVERT: a 33 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8984 (mm) REVERT: a 42 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7677 (ttp80) REVERT: a 115 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8386 (mm) REVERT: h 27 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7475 (tp-100) REVERT: h 66 ILE cc_start: 0.9017 (pt) cc_final: 0.8625 (mt) REVERT: h 100 PHE cc_start: 0.8414 (m-80) cc_final: 0.8179 (m-80) REVERT: k 35 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8373 (mpp80) outliers start: 39 outliers final: 20 residues processed: 270 average time/residue: 0.2891 time to fit residues: 104.9646 Evaluate side-chains 254 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 93 GLN Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 115 LEU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN k 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12721 Z= 0.215 Angle : 0.760 13.132 18448 Z= 0.421 Chirality : 0.038 0.192 2104 Planarity : 0.005 0.066 1319 Dihedral : 32.030 89.707 4127 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 6.03 % Allowed : 37.30 % Favored : 56.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 730 helix: 0.88 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.49 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 75 PHE 0.019 0.002 PHE b 62 TYR 0.037 0.002 TYR b 80 ARG 0.011 0.001 ARG b 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 32 GLU cc_start: 0.8193 (pp20) cc_final: 0.7810 (pp20) REVERT: H 98 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8019 (tt) REVERT: H 102 GLU cc_start: 0.8471 (pm20) cc_final: 0.8127 (pp20) REVERT: M 105 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7754 (mm-30) REVERT: a 33 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8954 (mm) REVERT: a 65 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8295 (mm) REVERT: h 27 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7499 (tp-100) REVERT: h 66 ILE cc_start: 0.9022 (pt) cc_final: 0.8625 (mt) REVERT: h 100 PHE cc_start: 0.8431 (m-80) cc_final: 0.8212 (m-80) REVERT: k 35 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8397 (mpp80) outliers start: 37 outliers final: 24 residues processed: 264 average time/residue: 0.2891 time to fit residues: 102.9143 Evaluate side-chains 265 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 41 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 35 ARG Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 53 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 0.0060 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN b 79 HIS ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 ASN k 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12721 Z= 0.214 Angle : 0.781 13.207 18448 Z= 0.429 Chirality : 0.038 0.244 2104 Planarity : 0.006 0.067 1319 Dihedral : 32.012 89.627 4127 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.54 % Allowed : 38.76 % Favored : 55.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.30), residues: 730 helix: 0.87 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.55 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 75 PHE 0.019 0.002 PHE b 62 TYR 0.036 0.002 TYR H 80 ARG 0.014 0.001 ARG b 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: H 30 ARG cc_start: 0.6290 (mtt180) cc_final: 0.6081 (mtt180) REVERT: H 32 GLU cc_start: 0.8214 (pp20) cc_final: 0.7791 (pp20) REVERT: H 40 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8524 (ptpp) REVERT: H 92 GLN cc_start: 0.8632 (tp40) cc_final: 0.8376 (tp40) REVERT: H 98 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8017 (tt) REVERT: H 102 GLU cc_start: 0.8451 (pm20) cc_final: 0.8093 (pp20) REVERT: M 105 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7787 (mm-30) REVERT: a 33 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8953 (mm) REVERT: a 65 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8316 (mm) REVERT: a 112 GLN cc_start: 0.6842 (tp40) cc_final: 0.6538 (tp40) REVERT: a 115 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8411 (mm) REVERT: b 113 LYS cc_start: 0.7745 (pptt) cc_final: 0.7517 (pptt) REVERT: h 27 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7538 (tp-100) REVERT: h 66 ILE cc_start: 0.9001 (pt) cc_final: 0.8593 (mt) REVERT: k 35 ARG cc_start: 0.8708 (tpp80) cc_final: 0.8452 (mpp80) outliers start: 34 outliers final: 24 residues processed: 261 average time/residue: 0.2719 time to fit residues: 97.0242 Evaluate side-chains 266 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 115 LEU Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 96 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 71 ARG Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 48 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 ASN b 79 HIS k 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12721 Z= 0.217 Angle : 0.790 14.401 18448 Z= 0.429 Chirality : 0.038 0.217 2104 Planarity : 0.006 0.071 1319 Dihedral : 31.976 89.966 4127 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.05 % Allowed : 38.93 % Favored : 56.03 % 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: 0.36 (0.30), residues: 730 helix: 0.91 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.47 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 75 PHE 0.026 0.002 PHE O 61 TYR 0.041 0.002 TYR b 80 ARG 0.013 0.001 ARG k 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ARG cc_start: 0.6376 (mtt180) cc_final: 0.6158 (mtt180) REVERT: H 32 GLU cc_start: 0.8331 (pp20) cc_final: 0.7915 (pp20) REVERT: H 40 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8526 (ptpp) REVERT: H 92 GLN cc_start: 0.8645 (tp40) cc_final: 0.8340 (tp40) REVERT: H 98 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7999 (tt) REVERT: H 102 GLU cc_start: 0.8456 (pm20) cc_final: 0.8106 (pp20) REVERT: M 105 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7779 (mm-30) REVERT: a 65 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8325 (mm) REVERT: b 113 LYS cc_start: 0.7730 (pptt) cc_final: 0.7491 (pptt) REVERT: h 27 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7591 (tp-100) REVERT: h 66 ILE cc_start: 0.8999 (pt) cc_final: 0.8587 (mt) REVERT: k 35 ARG cc_start: 0.8703 (tpp80) cc_final: 0.8453 (mpp80) outliers start: 31 outliers final: 25 residues processed: 256 average time/residue: 0.2716 time to fit residues: 94.6248 Evaluate side-chains 265 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain O residue 88 TYR Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 79 HIS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 81 ASP Chi-restraints excluded: chain f residue 94 GLU Chi-restraints excluded: chain f residue 106 ASP Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 118 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 40 ARG Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 HIS k 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.097071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.077992 restraints weight = 48666.134| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.04 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12721 Z= 0.233 Angle : 0.803 14.674 18448 Z= 0.436 Chirality : 0.038 0.208 2104 Planarity : 0.006 0.066 1319 Dihedral : 31.972 89.978 4127 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.05 % Allowed : 39.25 % Favored : 55.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.30), residues: 730 helix: 0.92 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS b 79 PHE 0.028 0.002 PHE O 61 TYR 0.038 0.003 TYR b 80 ARG 0.012 0.001 ARG k 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.35 seconds wall clock time: 57 minutes 29.20 seconds (3449.20 seconds total)