Starting phenix.real_space_refine on Fri Feb 16 19:47:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njw_12425/02_2024/7njw_12425.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njw_12425/02_2024/7njw_12425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njw_12425/02_2024/7njw_12425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njw_12425/02_2024/7njw_12425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njw_12425/02_2024/7njw_12425.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njw_12425/02_2024/7njw_12425.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5346 2.51 5 N 1316 2.21 5 O 1399 1.98 5 H 8337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 32": "OD1" <-> "OD2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 130": "OD1" <-> "OD2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 177": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Time building chain proxies: 7.38, per 1000 atoms: 0.45 Number of scatterers: 16426 At special positions: 0 Unit cell: (92.96, 78.02, 116.2, 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 28 16.00 O 1399 8.00 N 1316 7.00 C 5346 6.00 H 8337 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 87.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.662A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 80 removed outlier: 3.976A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.812A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.722A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 81 removed outlier: 4.898A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix Processing helix chain 'N' and resid 4 through 46 removed outlier: 4.025A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 81 removed outlier: 3.702A pdb=" N PHE N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.726A pdb=" N ILE N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.496A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 4.076A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.569A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 4.008A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.588A pdb=" N ALA P 66 " --> pdb=" O GLY P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.654A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 81 removed outlier: 4.143A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.968A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 80 removed outlier: 4.912A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix Processing helix chain 'S' and resid 4 through 46 removed outlier: 3.766A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.642A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.890A pdb=" N ILE S 59 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE S 80 " --> pdb=" O ALA S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.739A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 4.041A pdb=" N PHE T 54 " --> pdb=" O GLN T 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.542A pdb=" N ILE T 59 " --> pdb=" O THR T 55 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 51 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 107 Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.709A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.600A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 204 removed outlier: 3.610A pdb=" N ILE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.618A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 3.943A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.916A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.573A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 786 hydrogen bonds defined for protein. 2349 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 15.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8336 1.03 - 1.23: 13 1.23 - 1.42: 3347 1.42 - 1.62: 4843 1.62 - 1.81: 55 Bond restraints: 16594 Sorted by residual: bond pdb=" CB ILE L 40 " pdb=" CG2 ILE L 40 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.11e-01 bond pdb=" CG1 ILE L 20 " pdb=" CD1 ILE L 20 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.74e-01 bond pdb=" CA VAL b 50 " pdb=" CB VAL b 50 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.73e-01 bond pdb=" C GLN Q 50 " pdb=" O GLN Q 50 " ideal model delta sigma weight residual 1.236 1.246 -0.009 1.15e-02 7.56e+03 6.63e-01 bond pdb=" C THR O 55 " pdb=" O THR O 55 " ideal model delta sigma weight residual 1.244 1.237 0.007 9.10e-03 1.21e+04 6.52e-01 ... (remaining 16589 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.45: 248 106.45 - 113.32: 19640 113.32 - 120.20: 5658 120.20 - 127.07: 4495 127.07 - 133.94: 75 Bond angle restraints: 30116 Sorted by residual: angle pdb=" CA GLN Q 50 " pdb=" CB GLN Q 50 " pdb=" CG GLN Q 50 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 120.68 116.35 4.33 1.70e+00 3.46e-01 6.48e+00 angle pdb=" C VAL b 50 " pdb=" CA VAL b 50 " pdb=" CB VAL b 50 " ideal model delta sigma weight residual 114.00 110.69 3.31 1.31e+00 5.83e-01 6.38e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.33 -4.43 1.80e+00 3.09e-01 6.05e+00 angle pdb=" N GLN Q 50 " pdb=" CA GLN Q 50 " pdb=" CB GLN Q 50 " ideal model delta sigma weight residual 109.94 106.83 3.11 1.49e+00 4.50e-01 4.36e+00 ... (remaining 30111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6742 17.69 - 35.38: 601 35.38 - 53.07: 286 53.07 - 70.76: 124 70.76 - 88.45: 6 Dihedral angle restraints: 7759 sinusoidal: 4150 harmonic: 3609 Sorted by residual: dihedral pdb=" CA ASP a 130 " pdb=" CB ASP a 130 " pdb=" CG ASP a 130 " pdb=" OD1 ASP a 130 " ideal model delta sinusoidal sigma weight residual -30.00 -86.53 56.53 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU R 65 " pdb=" CG GLU R 65 " pdb=" CD GLU R 65 " pdb=" OE1 GLU R 65 " ideal model delta sinusoidal sigma weight residual 0.00 85.99 -85.99 1 3.00e+01 1.11e-03 9.92e+00 dihedral pdb=" CB GLU R 48 " pdb=" CG GLU R 48 " pdb=" CD GLU R 48 " pdb=" OE1 GLU R 48 " ideal model delta sinusoidal sigma weight residual 0.00 -85.38 85.38 1 3.00e+01 1.11e-03 9.81e+00 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 826 0.027 - 0.055: 273 0.055 - 0.082: 154 0.082 - 0.110: 60 0.110 - 0.137: 9 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA VAL a 58 " pdb=" N VAL a 58 " pdb=" C VAL a 58 " pdb=" CB VAL a 58 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE b 26 " pdb=" N ILE b 26 " pdb=" C ILE b 26 " pdb=" CB ILE b 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA PHE M 58 " pdb=" N PHE M 58 " pdb=" C PHE M 58 " pdb=" CB PHE M 58 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1319 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 50 " 0.010 2.00e-02 2.50e+03 1.58e-02 3.73e+00 pdb=" CD GLN Q 50 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 50 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 50 " 0.009 2.00e-02 2.50e+03 pdb="HE21 GLN Q 50 " 0.000 2.00e-02 2.50e+03 pdb="HE22 GLN Q 50 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY a 191 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C GLY a 191 " 0.025 2.00e-02 2.50e+03 pdb=" O GLY a 191 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN a 192 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 70 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ILE L 70 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE L 70 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN L 71 " -0.008 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 749 2.18 - 2.78: 33249 2.78 - 3.39: 50596 3.39 - 3.99: 62536 3.99 - 4.60: 99394 Nonbonded interactions: 246524 Sorted by model distance: nonbonded pdb=" OE1 GLN a 72 " pdb="HE21 GLN a 76 " model vdw 1.575 1.850 nonbonded pdb="HE22 GLN S 46 " pdb=" O ALA T 44 " model vdw 1.620 1.850 nonbonded pdb=" O PHE S 78 " pdb=" HG1 THR S 82 " model vdw 1.668 1.850 nonbonded pdb=" OE1 GLU P 48 " pdb=" H GLU P 48 " model vdw 1.674 1.850 nonbonded pdb=" O ASP b 70 " pdb=" HG SER b 74 " model vdw 1.690 1.850 ... (remaining 246519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 11.040 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: 0.250 Extract box with map and model: 25.420 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 57.890 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.036 8257 Z= 0.199 Angle : 0.504 6.098 11218 Z= 0.280 Chirality : 0.038 0.137 1322 Planarity : 0.004 0.032 1440 Dihedral : 14.130 88.454 2789 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.21 (0.27), residues: 1094 helix: 1.49 (0.18), residues: 942 sheet: -1.27 (1.82), residues: 10 loop : 2.11 (0.63), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.019 0.001 PHE M 58 TYR 0.008 0.001 TYR a 145 ARG 0.003 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 MET cc_start: 0.8269 (tmm) cc_final: 0.7822 (tmm) REVERT: a 84 LYS cc_start: 0.7107 (pttt) cc_final: 0.6859 (pttm) REVERT: d 46 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7631 (tm-30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.4204 time to fit residues: 61.4363 Evaluate side-chains 82 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8257 Z= 0.244 Angle : 0.521 5.364 11218 Z= 0.285 Chirality : 0.039 0.135 1322 Planarity : 0.004 0.038 1440 Dihedral : 3.632 15.235 1149 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.78 % Allowed : 4.66 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.26), residues: 1094 helix: 2.15 (0.17), residues: 951 sheet: -1.31 (1.82), residues: 10 loop : 2.83 (0.65), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.018 0.001 PHE M 58 TYR 0.027 0.001 TYR a 145 ARG 0.004 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 84 LYS cc_start: 0.7106 (pttt) cc_final: 0.6819 (pttm) outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.4131 time to fit residues: 50.6750 Evaluate side-chains 82 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 242 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.0040 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8257 Z= 0.220 Angle : 0.496 6.298 11218 Z= 0.267 Chirality : 0.038 0.135 1322 Planarity : 0.004 0.042 1440 Dihedral : 3.598 15.358 1149 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.04 % Allowed : 6.35 % 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: 3.69 (0.26), residues: 1094 helix: 2.46 (0.17), residues: 951 sheet: -1.30 (1.82), residues: 10 loop : 2.85 (0.65), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.018 0.001 PHE M 58 TYR 0.023 0.001 TYR a 145 ARG 0.003 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8663 (tmm) cc_final: 0.8327 (tmm) REVERT: a 84 LYS cc_start: 0.7097 (pttt) cc_final: 0.6822 (pttm) outliers start: 8 outliers final: 8 residues processed: 85 average time/residue: 0.4094 time to fit residues: 50.0182 Evaluate side-chains 81 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8257 Z= 0.230 Angle : 0.495 6.969 11218 Z= 0.265 Chirality : 0.038 0.134 1322 Planarity : 0.004 0.042 1440 Dihedral : 3.594 15.599 1149 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.30 % Allowed : 7.64 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.26), residues: 1094 helix: 2.58 (0.16), residues: 951 sheet: -1.31 (1.82), residues: 10 loop : 2.89 (0.65), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 PHE 0.017 0.001 PHE M 58 TYR 0.020 0.001 TYR a 145 ARG 0.003 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8640 (tmm) cc_final: 0.8245 (tmm) REVERT: a 84 LYS cc_start: 0.7108 (pttt) cc_final: 0.6836 (pttm) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.4027 time to fit residues: 48.6772 Evaluate side-chains 82 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8257 Z= 0.348 Angle : 0.546 7.301 11218 Z= 0.300 Chirality : 0.039 0.131 1322 Planarity : 0.004 0.046 1440 Dihedral : 3.739 16.088 1149 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.04 % Allowed : 8.81 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.25), residues: 1094 helix: 2.37 (0.16), residues: 951 sheet: -1.28 (1.90), residues: 10 loop : 2.72 (0.65), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.002 0.001 HIS d 58 PHE 0.018 0.002 PHE M 58 TYR 0.023 0.001 TYR a 145 ARG 0.003 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8639 (tmm) cc_final: 0.8216 (tmm) REVERT: Q 75 MET cc_start: 0.8628 (tmm) cc_final: 0.8306 (tmm) outliers start: 8 outliers final: 8 residues processed: 78 average time/residue: 0.4249 time to fit residues: 47.1228 Evaluate side-chains 78 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8257 Z= 0.240 Angle : 0.501 6.026 11218 Z= 0.270 Chirality : 0.038 0.136 1322 Planarity : 0.004 0.046 1440 Dihedral : 3.683 16.101 1149 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.30 % Allowed : 8.81 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.25), residues: 1094 helix: 2.76 (0.16), residues: 907 sheet: -1.17 (1.93), residues: 10 loop : 2.10 (0.56), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.018 0.001 PHE M 58 TYR 0.022 0.001 TYR a 145 ARG 0.002 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8648 (tmm) cc_final: 0.8231 (tmm) REVERT: Q 75 MET cc_start: 0.8651 (tmm) cc_final: 0.8300 (tmm) outliers start: 10 outliers final: 8 residues processed: 84 average time/residue: 0.4418 time to fit residues: 52.9330 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8257 Z= 0.236 Angle : 0.497 5.532 11218 Z= 0.268 Chirality : 0.038 0.135 1322 Planarity : 0.004 0.046 1440 Dihedral : 3.655 16.223 1149 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.30 % Allowed : 9.46 % Favored : 89.25 % 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: 4.00 (0.25), residues: 1094 helix: 2.81 (0.16), residues: 907 sheet: -1.23 (1.90), residues: 10 loop : 2.10 (0.56), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.017 0.001 PHE M 58 TYR 0.022 0.001 TYR a 145 ARG 0.002 0.000 ARG R 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8635 (tmm) cc_final: 0.8199 (tmm) REVERT: Q 75 MET cc_start: 0.8680 (tmm) cc_final: 0.8318 (tmm) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.4288 time to fit residues: 48.7961 Evaluate side-chains 81 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain T residue 59 ILE Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8257 Z= 0.244 Angle : 0.498 5.298 11218 Z= 0.268 Chirality : 0.038 0.140 1322 Planarity : 0.004 0.046 1440 Dihedral : 3.645 16.230 1149 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.17 % Allowed : 10.36 % Favored : 88.47 % 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: 4.02 (0.25), residues: 1094 helix: 2.83 (0.16), residues: 907 sheet: -1.27 (1.89), residues: 10 loop : 2.06 (0.55), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.018 0.001 PHE M 58 TYR 0.023 0.001 TYR a 145 ARG 0.001 0.000 ARG T 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8645 (tmm) cc_final: 0.8224 (tmm) REVERT: Q 75 MET cc_start: 0.8718 (tmm) cc_final: 0.8339 (tmm) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.4526 time to fit residues: 53.1300 Evaluate side-chains 82 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.0010 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8257 Z= 0.290 Angle : 0.519 7.502 11218 Z= 0.281 Chirality : 0.039 0.142 1322 Planarity : 0.004 0.047 1440 Dihedral : 3.695 16.391 1149 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.17 % Allowed : 10.88 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.25), residues: 1094 helix: 2.74 (0.16), residues: 907 sheet: -1.32 (1.90), residues: 10 loop : 1.97 (0.55), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.018 0.001 PHE M 58 TYR 0.023 0.001 TYR a 145 ARG 0.005 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: M 75 MET cc_start: 0.8639 (tmm) cc_final: 0.8204 (tmm) REVERT: Q 75 MET cc_start: 0.8744 (tmm) cc_final: 0.8381 (tmm) outliers start: 9 outliers final: 9 residues processed: 78 average time/residue: 0.4236 time to fit residues: 47.3574 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 67 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 GLN ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8257 Z= 0.175 Angle : 0.481 6.070 11218 Z= 0.254 Chirality : 0.039 0.136 1322 Planarity : 0.004 0.045 1440 Dihedral : 3.588 16.262 1149 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.04 % Allowed : 11.01 % Favored : 87.95 % 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: 4.25 (0.25), residues: 1094 helix: 2.99 (0.17), residues: 907 sheet: -1.20 (1.89), residues: 10 loop : 2.11 (0.55), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE M 58 TYR 0.021 0.001 TYR a 145 ARG 0.004 0.000 ARG M 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: M 75 MET cc_start: 0.8599 (tmm) cc_final: 0.8171 (tmm) REVERT: Q 75 MET cc_start: 0.8747 (tmm) cc_final: 0.8391 (tmm) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 0.4063 time to fit residues: 48.9784 Evaluate side-chains 83 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082491 restraints weight = 62024.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084785 restraints weight = 23145.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.086191 restraints weight = 10939.009| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8257 Z= 0.227 Angle : 0.494 5.607 11218 Z= 0.264 Chirality : 0.038 0.133 1322 Planarity : 0.004 0.043 1440 Dihedral : 3.584 16.315 1149 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.78 % Allowed : 11.27 % Favored : 87.95 % 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: 4.19 (0.25), residues: 1094 helix: 2.96 (0.16), residues: 907 sheet: -1.33 (1.87), residues: 10 loop : 2.05 (0.54), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.017 0.001 PHE M 58 TYR 0.022 0.001 TYR a 145 ARG 0.004 0.000 ARG M 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.75 seconds wall clock time: 61 minutes 4.70 seconds (3664.70 seconds total)