Starting phenix.real_space_refine on Tue Feb 13 07:04:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2024/7soa_25264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2024/7soa_25264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2024/7soa_25264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2024/7soa_25264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2024/7soa_25264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2024/7soa_25264.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.112 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2476 2.51 5 N 620 2.21 5 O 739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3850 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1994 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 234} Chain breaks: 5 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.59, per 1000 atoms: 0.67 Number of scatterers: 3850 At special positions: 0 Unit cell: (63.225, 85.143, 76.713, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 739 8.00 N 620 7.00 C 2476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 280 " " NAG A1303 " - " ASN A 163 " " NAG A1304 " - " ASN A 232 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 769.3 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 4.2% alpha, 55.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.970A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.681A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.826A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA A 262 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR A 95 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 199 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 201 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.386A pdb=" N THR A 272 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP A 288 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 274 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 286 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 276 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.990A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.614A pdb=" N PHE A 236 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 13.010A pdb=" N ASN A 137 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR A 238 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 240 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 369 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: 1.09 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 722 1.33 - 1.45: 1076 1.45 - 1.57: 2128 1.57 - 1.70: 2 1.70 - 1.82: 20 Bond restraints: 3948 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" CA SER A 155 " pdb=" CB SER A 155 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.22e+01 bond pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 1.530 1.592 -0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.472 -0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.38e+00 ... (remaining 3943 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.28: 140 107.28 - 113.98: 2096 113.98 - 120.67: 1697 120.67 - 127.37: 1401 127.37 - 134.07: 30 Bond angle restraints: 5364 Sorted by residual: angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.67 -7.64 9.90e-01 1.02e+00 5.96e+01 angle pdb=" C LEU A 214 " pdb=" N PRO A 215 " pdb=" CA PRO A 215 " ideal model delta sigma weight residual 120.03 127.11 -7.08 9.90e-01 1.02e+00 5.11e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 127.00 -7.15 1.01e+00 9.80e-01 5.01e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.76 126.92 -7.16 1.03e+00 9.43e-01 4.83e+01 ... (remaining 5359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2277 17.19 - 34.39: 83 34.39 - 51.58: 15 51.58 - 68.77: 7 68.77 - 85.96: 2 Dihedral angle restraints: 2384 sinusoidal: 998 harmonic: 1386 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.58 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" C LYS A 185 " pdb=" N LYS A 185 " pdb=" CA LYS A 185 " pdb=" CB LYS A 185 " ideal model delta harmonic sigma weight residual -122.60 -114.27 -8.33 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CB GLU A 189 " pdb=" CG GLU A 189 " pdb=" CD GLU A 189 " pdb=" OE1 GLU A 189 " ideal model delta sinusoidal sigma weight residual 0.00 85.96 -85.96 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 2381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 485 0.095 - 0.190: 94 0.190 - 0.285: 16 0.285 - 0.380: 8 0.380 - 0.475: 1 Chirality restraints: 604 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.93e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA LYS A 185 " pdb=" N LYS A 185 " pdb=" C LYS A 185 " pdb=" CB LYS A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 601 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.242 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG A1304 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 34 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ARG A 34 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY A 35 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 104 " -0.031 2.00e-02 2.50e+03 1.70e-02 5.79e+00 pdb=" CG TYR H 104 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR H 104 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR H 104 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 104 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR H 104 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 104 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 104 " -0.026 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 205 2.73 - 3.28: 3456 3.28 - 3.82: 6166 3.82 - 4.36: 8061 4.36 - 4.90: 13416 Nonbonded interactions: 31304 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.194 2.440 nonbonded pdb=" N THR A 29 " pdb=" O THR A 29 " model vdw 2.551 2.496 nonbonded pdb=" N SER A 151 " pdb=" O SER A 151 " model vdw 2.556 2.496 nonbonded pdb=" N GLY A 156 " pdb=" N VAL A 157 " model vdw 2.588 2.560 nonbonded pdb=" O ASP L 92 " pdb=" NH1 ARG H 103 " model vdw 2.595 2.520 ... (remaining 31299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 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: 26.860 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 15.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.011 0.062 3948 Z= 0.695 Angle : 1.273 11.028 5364 Z= 0.860 Chirality : 0.085 0.475 604 Planarity : 0.010 0.208 675 Dihedral : 10.148 85.964 1481 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.24 % Allowed : 0.73 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.99 (0.37), residues: 461 helix: 0.55 (1.59), residues: 11 sheet: 1.38 (0.37), residues: 184 loop : 0.20 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP H 47 HIS 0.001 0.001 HIS A 66 PHE 0.018 0.003 PHE A 55 TYR 0.031 0.004 TYR H 104 ARG 0.004 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.443 Fit side-chains REVERT: A 154 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7276 (tp30) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1940 time to fit residues: 19.6118 Evaluate side-chains 57 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3948 Z= 0.303 Angle : 0.671 13.500 5364 Z= 0.338 Chirality : 0.049 0.201 604 Planarity : 0.005 0.048 675 Dihedral : 6.533 54.143 644 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.91 % Allowed : 4.85 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.38), residues: 461 helix: 2.91 (1.64), residues: 11 sheet: 1.41 (0.36), residues: 193 loop : 0.18 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.003 0.001 HIS A 66 PHE 0.016 0.002 PHE A 133 TYR 0.015 0.001 TYR H 95 ARG 0.005 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.428 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.1593 time to fit residues: 11.1542 Evaluate side-chains 52 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 37 optimal weight: 0.3980 chunk 14 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3948 Z= 0.167 Angle : 0.533 6.566 5364 Z= 0.274 Chirality : 0.046 0.334 604 Planarity : 0.004 0.038 675 Dihedral : 5.336 56.723 641 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.94 % Allowed : 7.04 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.39), residues: 461 helix: 3.17 (1.70), residues: 11 sheet: 1.49 (0.37), residues: 187 loop : 0.17 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE A 55 TYR 0.016 0.001 TYR A 168 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.426 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1871 time to fit residues: 11.8424 Evaluate side-chains 48 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3948 Z= 0.256 Angle : 0.551 9.545 5364 Z= 0.283 Chirality : 0.045 0.147 604 Planarity : 0.004 0.034 675 Dihedral : 5.255 48.513 641 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.18 % Allowed : 6.80 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.39), residues: 461 helix: 3.01 (1.65), residues: 11 sheet: 1.46 (0.37), residues: 191 loop : 0.13 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.003 0.001 HIS A 205 PHE 0.019 0.002 PHE A 133 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.425 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 53 average time/residue: 0.1637 time to fit residues: 11.0775 Evaluate side-chains 55 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 14 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3948 Z= 0.154 Angle : 0.502 8.866 5364 Z= 0.258 Chirality : 0.044 0.199 604 Planarity : 0.004 0.034 675 Dihedral : 4.573 24.678 641 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 7.52 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.39), residues: 461 helix: 3.03 (1.65), residues: 11 sheet: 1.48 (0.36), residues: 200 loop : 0.09 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 133 TYR 0.016 0.001 TYR A 168 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.443 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.1657 time to fit residues: 10.9642 Evaluate side-chains 49 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3948 Z= 0.179 Angle : 0.508 8.449 5364 Z= 0.259 Chirality : 0.044 0.164 604 Planarity : 0.004 0.034 675 Dihedral : 4.545 27.761 641 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.91 % Allowed : 7.28 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.40), residues: 461 helix: 2.97 (1.64), residues: 11 sheet: 1.41 (0.36), residues: 206 loop : 0.11 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE A 133 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.448 Fit side-chains REVERT: A 302 LYS cc_start: 0.8351 (mmtp) cc_final: 0.7696 (mmmt) outliers start: 12 outliers final: 9 residues processed: 51 average time/residue: 0.1583 time to fit residues: 10.4059 Evaluate side-chains 53 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3948 Z= 0.245 Angle : 0.548 10.124 5364 Z= 0.278 Chirality : 0.046 0.188 604 Planarity : 0.004 0.034 675 Dihedral : 4.713 24.419 641 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.16 % Allowed : 7.77 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.39), residues: 461 helix: 2.97 (1.64), residues: 11 sheet: 1.48 (0.38), residues: 196 loop : 0.00 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.002 PHE A 133 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.438 Fit side-chains REVERT: A 302 LYS cc_start: 0.8365 (mmtp) cc_final: 0.7720 (mmmt) outliers start: 13 outliers final: 12 residues processed: 56 average time/residue: 0.1483 time to fit residues: 10.7385 Evaluate side-chains 59 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3948 Z= 0.201 Angle : 0.513 9.280 5364 Z= 0.263 Chirality : 0.044 0.140 604 Planarity : 0.004 0.035 675 Dihedral : 4.766 32.089 641 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.91 % Allowed : 8.25 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.39), residues: 461 helix: 2.91 (1.64), residues: 11 sheet: 1.47 (0.38), residues: 196 loop : -0.00 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.002 PHE A 133 TYR 0.011 0.001 TYR H 95 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.429 Fit side-chains REVERT: A 302 LYS cc_start: 0.8352 (mmtp) cc_final: 0.7717 (mmmt) outliers start: 12 outliers final: 12 residues processed: 54 average time/residue: 0.1489 time to fit residues: 10.4683 Evaluate side-chains 57 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.0050 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 overall best weight: 0.1348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3948 Z= 0.112 Angle : 0.446 5.461 5364 Z= 0.233 Chirality : 0.042 0.135 604 Planarity : 0.004 0.035 675 Dihedral : 4.442 35.549 641 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.43 % Allowed : 8.74 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.40), residues: 461 helix: 2.70 (1.65), residues: 11 sheet: 1.45 (0.36), residues: 209 loop : 0.03 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 3 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 133 TYR 0.009 0.001 TYR H 95 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.427 Fit side-chains REVERT: A 302 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7690 (mmmt) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.1413 time to fit residues: 11.4156 Evaluate side-chains 62 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0070 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.0570 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3948 Z= 0.161 Angle : 0.478 5.805 5364 Z= 0.248 Chirality : 0.043 0.137 604 Planarity : 0.004 0.034 675 Dihedral : 4.449 34.830 641 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.94 % Allowed : 9.22 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.40), residues: 461 helix: 2.73 (1.62), residues: 11 sheet: 1.55 (0.37), residues: 206 loop : 0.02 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.001 PHE A 133 TYR 0.021 0.001 TYR A 168 ARG 0.002 0.000 ARG A 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.415 Fit side-chains REVERT: A 302 LYS cc_start: 0.8330 (mmtp) cc_final: 0.7700 (mmmt) outliers start: 8 outliers final: 8 residues processed: 54 average time/residue: 0.1483 time to fit residues: 10.4110 Evaluate side-chains 57 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099219 restraints weight = 4126.788| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.05 r_work: 0.2895 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3948 Z= 0.254 Angle : 0.547 9.561 5364 Z= 0.279 Chirality : 0.045 0.143 604 Planarity : 0.004 0.035 675 Dihedral : 4.713 29.617 641 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.18 % Allowed : 9.22 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.40), residues: 461 helix: 2.99 (1.64), residues: 11 sheet: 1.54 (0.38), residues: 196 loop : -0.00 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.002 PHE A 133 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.04 seconds wall clock time: 30 minutes 42.17 seconds (1842.17 seconds total)