Starting phenix.real_space_refine on Mon Nov 13 18:19:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2023/7soa_25264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2023/7soa_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_25264/11_2023/7soa_25264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2023/7soa_25264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2023/7soa_25264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2023/7soa_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-1.21rc1-5144/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 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 chiralities: 4 Time building chain proxies: 2.44, per 1000 atoms: 0.63 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: 1.42 Conformation dependent library (CDL) restraints added in 725.6 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: 0.45 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: 1.06 Time building geometry restraints manager: 1.54 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: 2161 17.19 - 34.39: 73 34.39 - 51.58: 15 51.58 - 68.77: 7 68.77 - 85.96: 2 Dihedral angle restraints: 2258 sinusoidal: 872 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 2255 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: 7.830 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: 27.810 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.450 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.940 ------------------------------------------------------------------------------- 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 : 10.315 85.964 1355 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 *********************** 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 : 0.441 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1862 time to fit residues: 18.8895 Evaluate side-chains 56 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3948 Z= 0.296 Angle : 0.655 14.948 5364 Z= 0.328 Chirality : 0.048 0.168 604 Planarity : 0.005 0.045 675 Dihedral : 4.708 15.565 515 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.18 % Allowed : 6.07 % Favored : 91.75 % 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 (0.38), residues: 461 helix: 2.84 (1.62), residues: 11 sheet: 1.42 (0.36), residues: 193 loop : 0.17 (0.38), residues: 257 *********************** 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 64 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.449 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.1386 time to fit residues: 10.9040 Evaluate side-chains 50 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0463 time to fit residues: 0.9481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2625 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= 0.185 Angle : 0.566 12.078 5364 Z= 0.282 Chirality : 0.046 0.372 604 Planarity : 0.004 0.038 675 Dihedral : 4.321 15.631 515 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.46 % Allowed : 7.28 % Favored : 91.26 % 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: 1.20 (0.39), residues: 461 helix: 3.25 (1.71), residues: 11 sheet: 1.55 (0.37), residues: 193 loop : 0.13 (0.38), residues: 257 *********************** 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: 6 poor density : 49 time to evaluate : 0.421 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.1685 time to fit residues: 11.1302 Evaluate side-chains 50 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0404 time to fit residues: 0.8670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 44 optimal weight: 0.1980 chunk 39 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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: 0.8290 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3948 Z= 0.156 Angle : 0.505 8.370 5364 Z= 0.257 Chirality : 0.044 0.215 604 Planarity : 0.004 0.034 675 Dihedral : 4.200 15.029 515 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.97 % Allowed : 7.04 % Favored : 91.99 % 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: 1.21 (0.39), residues: 461 helix: 2.92 (1.64), residues: 11 sheet: 1.56 (0.37), residues: 190 loop : 0.17 (0.40), residues: 260 *********************** 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 60 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.431 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.1526 time to fit residues: 11.1683 Evaluate side-chains 51 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0434 time to fit residues: 0.8890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3948 Z= 0.367 Angle : 0.642 12.190 5364 Z= 0.315 Chirality : 0.052 0.442 604 Planarity : 0.004 0.035 675 Dihedral : 4.613 15.979 515 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.21 % Allowed : 7.52 % Favored : 91.26 % 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 (0.39), residues: 461 helix: 2.82 (1.62), residues: 11 sheet: 1.53 (0.37), residues: 191 loop : -0.11 (0.38), residues: 259 *********************** 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 53 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.419 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.1538 time to fit residues: 10.3406 Evaluate side-chains 48 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0416 time to fit residues: 0.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 23 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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: 0.8348 moved from start: 0.3466 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= 0.214 Angle : 0.549 10.740 5364 Z= 0.273 Chirality : 0.047 0.372 604 Planarity : 0.004 0.035 675 Dihedral : 4.399 15.613 515 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.73 % Allowed : 8.25 % 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: 1.03 (0.39), residues: 461 helix: 3.00 (1.65), residues: 11 sheet: 1.54 (0.38), residues: 191 loop : -0.06 (0.38), residues: 259 *********************** 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 51 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.392 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.1668 time to fit residues: 10.5328 Evaluate side-chains 48 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0591 time to fit residues: 0.6982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8387 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3948 Z= 0.352 Angle : 0.618 12.285 5364 Z= 0.307 Chirality : 0.049 0.304 604 Planarity : 0.004 0.036 675 Dihedral : 4.638 16.310 515 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.21 % Allowed : 8.50 % Favored : 90.29 % 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: 0.86 (0.39), residues: 461 helix: 2.92 (1.64), residues: 11 sheet: 1.45 (0.38), residues: 191 loop : -0.21 (0.38), residues: 259 *********************** 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 56 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.419 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.1754 time to fit residues: 11.9749 Evaluate side-chains 53 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0476 time to fit residues: 0.9107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3948 Z= 0.214 Angle : 0.545 11.085 5364 Z= 0.271 Chirality : 0.046 0.281 604 Planarity : 0.004 0.036 675 Dihedral : 4.403 15.932 515 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.49 % Allowed : 8.98 % 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: 0.87 (0.39), residues: 461 helix: 3.01 (1.66), residues: 11 sheet: 1.44 (0.38), residues: 191 loop : -0.18 (0.38), residues: 259 *********************** 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 51 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.572 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.1957 time to fit residues: 12.2342 Evaluate side-chains 49 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0693 time to fit residues: 1.0541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3948 Z= 0.242 Angle : 0.554 10.895 5364 Z= 0.275 Chirality : 0.046 0.253 604 Planarity : 0.004 0.036 675 Dihedral : 4.386 16.023 515 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.49 % Allowed : 8.98 % 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: 0.90 (0.39), residues: 461 helix: 3.03 (1.65), residues: 11 sheet: 1.40 (0.38), residues: 196 loop : -0.15 (0.39), residues: 254 *********************** 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 51 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.398 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.1781 time to fit residues: 11.2289 Evaluate side-chains 47 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.8352 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3948 Z= 0.202 Angle : 0.527 9.683 5364 Z= 0.264 Chirality : 0.045 0.248 604 Planarity : 0.004 0.035 675 Dihedral : 4.306 15.796 515 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % 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: 0.92 (0.39), residues: 461 helix: 3.05 (1.65), residues: 11 sheet: 1.40 (0.38), residues: 196 loop : -0.12 (0.39), residues: 254 ********************** 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 47 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.400 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1765 time to fit residues: 10.4528 Evaluate side-chains 45 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.102747 restraints weight = 4083.326| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.09 r_work: 0.2792 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3948 Z= 0.191 Angle : 0.519 9.313 5364 Z= 0.261 Chirality : 0.045 0.247 604 Planarity : 0.004 0.035 675 Dihedral : 4.236 15.643 515 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.24 % Allowed : 9.71 % Favored : 90.05 % 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: 0.93 (0.39), residues: 461 helix: 2.96 (1.64), residues: 11 sheet: 1.40 (0.38), residues: 196 loop : -0.10 (0.39), residues: 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1646.92 seconds wall clock time: 30 minutes 8.64 seconds (1808.64 seconds total)