Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 20:37:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/07_2023/7zyl_15026_trim_updated.pdb" } resolution = 2.08 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= 0.000 sd= 0.005 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 20 5.16 5 C 2504 2.51 5 N 684 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 133": "OD1" <-> "OD2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ASP 133": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3992 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: "F" 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: "G" 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: "H" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.47, per 1000 atoms: 0.62 Number of scatterers: 3992 At special positions: 0 Unit cell: (62.55, 72.45, 66.15, 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 20 16.00 O 784 8.00 N 684 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 107 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 41 " " NAG F 1 " - " ASN B 41 " " NAG G 1 " - " ASN C 41 " " NAG H 1 " - " ASN D 41 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 584.9 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 4 sheets defined 6.8% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 130 through 135 removed outlier: 4.617A pdb=" N TRP A 134 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 130 through 135 removed outlier: 4.599A pdb=" N TRP B 134 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 130 through 135 removed outlier: 4.597A pdb=" N TRP C 134 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 4.602A pdb=" N TRP D 134 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.410A pdb=" N ARG A 146 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU A 115 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 41 through 44 removed outlier: 4.419A pdb=" N ARG B 146 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU B 115 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 41 through 44 removed outlier: 4.291A pdb=" N ARG C 146 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLU C 115 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 41 through 44 removed outlier: 4.419A pdb=" N ARG D 146 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU D 115 " --> pdb=" O ARG D 146 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 492 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: 1.19 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 636 1.30 - 1.43: 1052 1.43 - 1.56: 2340 1.56 - 1.68: 16 1.68 - 1.81: 28 Bond restraints: 4072 Sorted by residual: bond pdb=" N27 KFL B 201 " pdb=" O28 KFL B 201 " ideal model delta sigma weight residual 1.404 1.171 0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" N27 KFL A 201 " pdb=" O28 KFL A 201 " ideal model delta sigma weight residual 1.404 1.172 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" N27 KFL D 201 " pdb=" O28 KFL D 201 " ideal model delta sigma weight residual 1.404 1.173 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" N27 KFL C 201 " pdb=" O28 KFL C 201 " ideal model delta sigma weight residual 1.404 1.173 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C02 KFL D 201 " pdb=" N27 KFL D 201 " ideal model delta sigma weight residual 1.494 1.439 0.055 2.00e-02 2.50e+03 7.52e+00 ... (remaining 4067 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.42: 154 107.42 - 114.07: 2456 114.07 - 120.72: 1362 120.72 - 127.37: 1520 127.37 - 134.02: 44 Bond angle restraints: 5536 Sorted by residual: angle pdb=" N ASN D 41 " pdb=" CA ASN D 41 " pdb=" C ASN D 41 " ideal model delta sigma weight residual 110.52 107.14 3.38 1.48e+00 4.57e-01 5.21e+00 angle pdb=" N ASN A 81 " pdb=" CA ASN A 81 " pdb=" CB ASN A 81 " ideal model delta sigma weight residual 113.65 110.31 3.34 1.47e+00 4.63e-01 5.15e+00 angle pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" CB ILE A 68 " ideal model delta sigma weight residual 110.13 113.67 -3.54 1.56e+00 4.11e-01 5.14e+00 angle pdb=" N ASN A 41 " pdb=" CA ASN A 41 " pdb=" C ASN A 41 " ideal model delta sigma weight residual 110.32 106.79 3.53 1.59e+00 3.96e-01 4.93e+00 angle pdb=" N ASN B 41 " pdb=" CA ASN B 41 " pdb=" C ASN B 41 " ideal model delta sigma weight residual 110.32 106.86 3.46 1.59e+00 3.96e-01 4.72e+00 ... (remaining 5531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2009 17.77 - 35.54: 197 35.54 - 53.31: 37 53.31 - 71.08: 17 71.08 - 88.84: 16 Dihedral angle restraints: 2276 sinusoidal: 920 harmonic: 1356 Sorted by residual: dihedral pdb=" CB GLU C 115 " pdb=" CG GLU C 115 " pdb=" CD GLU C 115 " pdb=" OE1 GLU C 115 " ideal model delta sinusoidal sigma weight residual 0.00 -88.84 88.84 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU D 115 " pdb=" CG GLU D 115 " pdb=" CD GLU D 115 " pdb=" OE1 GLU D 115 " ideal model delta sinusoidal sigma weight residual 0.00 -87.59 87.59 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" C09 KFL A 201 " pdb=" C10 KFL A 201 " pdb=" C11 KFL A 201 " pdb=" C12 KFL A 201 " ideal model delta sinusoidal sigma weight residual -162.95 -75.44 -87.51 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 2273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 543 0.055 - 0.110: 94 0.110 - 0.165: 11 0.165 - 0.221: 0 0.221 - 0.276: 8 Chirality restraints: 656 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 41 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 41 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 41 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 653 not shown) Planarity restraints: 676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 41 " 0.027 2.00e-02 2.50e+03 2.46e-02 7.55e+00 pdb=" CG ASN C 41 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 41 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 41 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 41 " -0.026 2.00e-02 2.50e+03 2.38e-02 7.10e+00 pdb=" CG ASN A 41 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 41 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 41 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 41 " -0.026 2.00e-02 2.50e+03 2.37e-02 7.01e+00 pdb=" CG ASN D 41 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN D 41 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 41 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.026 2.00e-02 2.50e+03 ... (remaining 673 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 79 2.66 - 3.22: 3658 3.22 - 3.78: 6728 3.78 - 4.34: 9635 4.34 - 4.90: 15038 Nonbonded interactions: 35138 Sorted by model distance: nonbonded pdb=" OE2 GLU C 98 " pdb=" ND2 ASN D 81 " model vdw 2.104 2.520 nonbonded pdb=" OG SER C 40 " pdb=" O20 KFL C 201 " model vdw 2.329 2.440 nonbonded pdb=" OG SER B 40 " pdb=" O20 KFL B 201 " model vdw 2.337 2.440 nonbonded pdb=" OG SER A 40 " pdb=" O20 KFL A 201 " model vdw 2.338 2.440 nonbonded pdb=" OG SER D 40 " pdb=" O20 KFL D 201 " model vdw 2.338 2.440 ... (remaining 35133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.010 Normalize map: mean=0, sd=1: 3.290 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: 11.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.410 Find NCS groups from input model: 0.270 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 0.233 4072 Z= 0.566 Angle : 0.623 5.498 5536 Z= 0.312 Chirality : 0.052 0.276 656 Planarity : 0.003 0.024 672 Dihedral : 17.591 88.845 1392 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.36), residues: 476 helix: -4.93 (0.17), residues: 24 sheet: 0.53 (0.26), residues: 288 loop : 1.26 (0.50), residues: 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.4407 time to fit residues: 100.8967 Evaluate side-chains 66 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8782 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.021 4072 Z= 0.290 Angle : 0.685 4.957 5536 Z= 0.354 Chirality : 0.048 0.184 656 Planarity : 0.004 0.031 672 Dihedral : 13.965 80.420 548 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.36), residues: 476 helix: -4.92 (0.18), residues: 24 sheet: 0.44 (0.27), residues: 288 loop : 1.33 (0.49), residues: 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.487 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 78 average time/residue: 1.3988 time to fit residues: 112.3432 Evaluate side-chains 74 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1686 time to fit residues: 0.7639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 4072 Z= 0.211 Angle : 0.637 4.569 5536 Z= 0.328 Chirality : 0.046 0.172 656 Planarity : 0.004 0.024 672 Dihedral : 13.783 76.686 548 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.37), residues: 476 helix: -4.86 (0.18), residues: 24 sheet: 0.32 (0.27), residues: 292 loop : 1.32 (0.51), residues: 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 1.4326 time to fit residues: 109.1468 Evaluate side-chains 73 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 41 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 4072 Z= 0.148 Angle : 0.588 4.722 5536 Z= 0.300 Chirality : 0.044 0.161 656 Planarity : 0.003 0.018 672 Dihedral : 13.512 74.452 548 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.37), residues: 476 helix: -4.84 (0.18), residues: 24 sheet: 0.36 (0.27), residues: 292 loop : 1.31 (0.49), residues: 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 77 average time/residue: 1.4123 time to fit residues: 111.9951 Evaluate side-chains 72 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1603 time to fit residues: 0.8176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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: 0.8799 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.032 4072 Z= 0.445 Angle : 0.747 5.098 5536 Z= 0.391 Chirality : 0.052 0.171 656 Planarity : 0.005 0.039 672 Dihedral : 14.605 82.323 548 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.36), residues: 476 helix: -4.87 (0.19), residues: 24 sheet: 0.28 (0.27), residues: 292 loop : 1.22 (0.51), residues: 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.660 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 1.4423 time to fit residues: 105.4718 Evaluate side-chains 70 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8761 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.016 4072 Z= 0.184 Angle : 0.613 4.874 5536 Z= 0.318 Chirality : 0.046 0.142 656 Planarity : 0.004 0.023 672 Dihedral : 13.913 76.903 548 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.37), residues: 476 helix: -4.85 (0.18), residues: 24 sheet: 0.35 (0.27), residues: 292 loop : 1.25 (0.50), residues: 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 77 average time/residue: 1.5314 time to fit residues: 121.2154 Evaluate side-chains 71 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1649 time to fit residues: 0.8142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.1980 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.8781 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.021 4072 Z= 0.288 Angle : 0.663 5.158 5536 Z= 0.346 Chirality : 0.047 0.142 656 Planarity : 0.004 0.031 672 Dihedral : 14.283 79.516 548 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.37), residues: 476 helix: -4.85 (0.19), residues: 24 sheet: 0.32 (0.27), residues: 292 loop : 1.25 (0.51), residues: 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.487 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 1.4968 time to fit residues: 107.8112 Evaluate side-chains 70 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8750 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 4072 Z= 0.152 Angle : 0.590 5.032 5536 Z= 0.305 Chirality : 0.045 0.125 656 Planarity : 0.003 0.021 672 Dihedral : 13.726 74.703 548 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.36), residues: 476 helix: -4.84 (0.18), residues: 24 sheet: 0.36 (0.27), residues: 292 loop : 1.30 (0.49), residues: 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 1.5874 time to fit residues: 120.6203 Evaluate side-chains 73 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1624 time to fit residues: 0.7896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8786 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.024 4072 Z= 0.329 Angle : 0.689 5.331 5536 Z= 0.360 Chirality : 0.048 0.136 656 Planarity : 0.005 0.032 672 Dihedral : 14.425 80.514 548 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.37), residues: 476 helix: -4.86 (0.19), residues: 24 sheet: 0.32 (0.27), residues: 292 loop : 1.30 (0.51), residues: 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 1.3843 time to fit residues: 102.6772 Evaluate side-chains 70 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8741 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4072 Z= 0.145 Angle : 0.587 5.085 5536 Z= 0.302 Chirality : 0.044 0.155 656 Planarity : 0.003 0.020 672 Dihedral : 13.627 73.534 548 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.36), residues: 476 helix: -4.83 (0.18), residues: 24 sheet: 0.38 (0.27), residues: 292 loop : 1.28 (0.49), residues: 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 1.5009 time to fit residues: 114.2768 Evaluate side-chains 73 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.3980 chunk 15 optimal weight: 0.1980 chunk 39 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.124143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101572 restraints weight = 4618.886| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.28 r_work: 0.3191 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 4072 Z= 0.124 Angle : 0.579 5.164 5536 Z= 0.294 Chirality : 0.044 0.153 656 Planarity : 0.003 0.018 672 Dihedral : 13.301 70.611 548 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.36), residues: 476 helix: -4.83 (0.18), residues: 24 sheet: 0.35 (0.27), residues: 300 loop : 1.51 (0.50), residues: 152 =============================================================================== Job complete usr+sys time: 2355.90 seconds wall clock time: 42 minutes 26.45 seconds (2546.45 seconds total)