Starting phenix.real_space_refine (version: dev) on Fri Feb 17 07:16:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2023/7soa_25264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_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_25264/02_2023/7soa_25264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2023/7soa_25264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2023/7soa_25264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/02_2023/7soa_25264.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 2.83, per 1000 atoms: 0.74 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: 1.49 Conformation dependent library (CDL) restraints added in 676.4 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: 0.31 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: 1.63 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=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.435 1.472 -0.037 1.10e-02 8.26e+03 1.12e+01 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.435 1.471 -0.036 1.10e-02 8.26e+03 1.06e+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 ... (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: 2197 17.19 - 34.39: 73 34.39 - 51.58: 15 51.58 - 68.77: 7 68.77 - 85.96: 2 Dihedral angle restraints: 2294 sinusoidal: 908 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 2291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 485 0.095 - 0.190: 98 0.190 - 0.285: 12 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 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. 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: 7.370 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: 0.010 Extract box with map and model: 30.120 Check model and map are aligned: 0.070 Process input model: 15.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.010 0.062 3948 Z= 0.671 Angle : 1.258 11.028 5364 Z= 0.886 Chirality : 0.083 0.475 604 Planarity : 0.010 0.208 675 Dihedral : 10.279 85.964 1391 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 % 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 : 0.460 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1931 time to fit residues: 19.5148 Evaluate side-chains 56 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6163 ------------------------------------------------------------------------------- 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 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 3948 Z= 0.296 Angle : 0.599 5.662 5364 Z= 0.322 Chirality : 0.046 0.153 604 Planarity : 0.005 0.047 675 Dihedral : 4.979 15.708 551 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.91 % 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: 1.41 (0.36), residues: 193 loop : 0.19 (0.37), 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 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.444 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 0.1409 time to fit residues: 11.4412 Evaluate side-chains 51 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0409 time to fit residues: 0.9515 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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: 0.8704 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3948 Z= 0.288 Angle : 0.564 9.838 5364 Z= 0.297 Chirality : 0.045 0.141 604 Planarity : 0.004 0.040 675 Dihedral : 4.818 16.246 551 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.70 % 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: 3.16 (1.69), residues: 11 sheet: 1.47 (0.36), residues: 199 loop : -0.06 (0.39), residues: 251 *********************** 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 54 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.460 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.1914 time to fit residues: 12.4397 Evaluate side-chains 48 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0422 time to fit residues: 0.9224 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 3948 Z= 0.311 Angle : 0.565 10.356 5364 Z= 0.292 Chirality : 0.046 0.143 604 Planarity : 0.004 0.036 675 Dihedral : 4.812 16.392 551 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.70 % 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: 1.02 (0.39), residues: 461 helix: 2.90 (1.64), residues: 11 sheet: 1.44 (0.36), residues: 200 loop : -0.05 (0.39), residues: 250 *********************** 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 55 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.456 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.1868 time to fit residues: 11.6824 Evaluate side-chains 51 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0495 time to fit residues: 1.0891 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8752 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 3948 Z= 0.371 Angle : 0.597 11.755 5364 Z= 0.306 Chirality : 0.047 0.147 604 Planarity : 0.004 0.037 675 Dihedral : 4.914 16.552 551 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.21 % 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: 2.85 (1.65), residues: 11 sheet: 1.43 (0.37), residues: 192 loop : -0.18 (0.37), residues: 258 *********************** 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 : 0.496 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.1570 time to fit residues: 10.6040 Evaluate side-chains 48 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0465 time to fit residues: 0.7764 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8735 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3948 Z= 0.265 Angle : 0.547 11.342 5364 Z= 0.281 Chirality : 0.045 0.143 604 Planarity : 0.004 0.036 675 Dihedral : 4.766 16.128 551 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.97 % 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 (1.66), residues: 11 sheet: 1.39 (0.38), residues: 192 loop : -0.16 (0.38), residues: 258 *********************** 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 53 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.428 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.1516 time to fit residues: 10.1111 Evaluate side-chains 49 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0403 time to fit residues: 0.7593 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 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: 0.7582 ------------------------------------------------------------------------------- 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: 0.8745 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 3948 Z= 0.308 Angle : 0.576 11.658 5364 Z= 0.296 Chirality : 0.046 0.145 604 Planarity : 0.004 0.036 675 Dihedral : 4.813 16.468 551 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.49 % 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: 0.76 (0.39), residues: 461 helix: 2.75 (1.65), residues: 11 sheet: 1.34 (0.38), residues: 192 loop : -0.24 (0.38), residues: 258 *********************** 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 47 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.446 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1574 time to fit residues: 9.4769 Evaluate side-chains 46 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0391 time to fit residues: 0.6755 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8729 moved from start: 0.3848 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= 0.235 Angle : 0.526 10.302 5364 Z= 0.272 Chirality : 0.044 0.143 604 Planarity : 0.004 0.035 675 Dihedral : 4.677 15.964 551 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.24 % 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: 0.81 (0.39), residues: 461 helix: 2.88 (1.66), residues: 11 sheet: 1.40 (0.38), residues: 191 loop : -0.23 (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 43 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.449 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1496 time to fit residues: 8.5410 Evaluate side-chains 42 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6124 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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: 0.8710 moved from start: 0.3867 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= 0.175 Angle : 0.495 8.688 5364 Z= 0.257 Chirality : 0.043 0.139 604 Planarity : 0.004 0.035 675 Dihedral : 4.540 15.687 551 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.00 % 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: 0.89 (0.39), residues: 461 helix: 2.84 (1.65), residues: 11 sheet: 1.38 (0.38), residues: 196 loop : -0.13 (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 49 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.413 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1623 time to fit residues: 10.2695 Evaluate side-chains 43 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8967 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 overall best weight: 0.2724 ------------------------------------------------------------------------------- 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: 0.8692 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3948 Z= 0.145 Angle : 0.470 7.076 5364 Z= 0.246 Chirality : 0.042 0.137 604 Planarity : 0.004 0.034 675 Dihedral : 4.420 15.445 551 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.24 % 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: 0.97 (0.40), residues: 461 helix: 2.81 (1.64), residues: 11 sheet: 1.41 (0.37), residues: 197 loop : -0.05 (0.39), residues: 253 ********************** 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 44 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.381 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1605 time to fit residues: 8.8228 Evaluate side-chains 43 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0395 time to fit residues: 0.6011 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.125014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.097088 restraints weight = 4181.154| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.02 r_work: 0.2738 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3964 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= 0.335 Angle : 0.575 10.667 5364 Z= 0.295 Chirality : 0.046 0.145 604 Planarity : 0.004 0.035 675 Dihedral : 4.767 16.052 551 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.00 % 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: 0.89 (0.40), residues: 461 helix: 2.90 (1.64), residues: 11 sheet: 1.36 (0.38), residues: 196 loop : -0.11 (0.39), residues: 254 =============================================================================== Job complete usr+sys time: 1590.96 seconds wall clock time: 29 minutes 35.68 seconds (1775.68 seconds total)