Starting phenix.real_space_refine (version: dev) on Tue Feb 21 16:08:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c4h_7340/02_2023/6c4h_7340_updated.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= 0.000 sd= 0.012 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 "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "v ARG 256": "NH1" <-> "NH2" Residue "v ARG 262": "NH1" <-> "NH2" 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: 15326 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 13622 Classifications: {'RNA': 636} Modifications used: {'rna2p': 4, 'rna2p_pur': 71, 'rna2p_pyr': 31, 'rna3p': 13, 'rna3p_pur': 274, 'rna3p_pyr': 243} Link IDs: {'rna2p': 106, 'rna3p': 529} Chain breaks: 9 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 5, 'TRANS': 41} Chain: "D" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 361 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "N" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 125 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "x" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna3p': 11} Chain breaks: 1 Chain: "v" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 496 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Unusual residues: {' MG': 34} Classifications: {'undetermined': 34} Link IDs: {None: 33} Time building chain proxies: 9.49, per 1000 atoms: 0.62 Number of scatterers: 15326 At special positions: 0 Unit cell: (132, 104.4, 133.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 6 16.00 P 647 15.00 Mg 34 11.99 O 4765 8.00 N 2808 7.00 C 7066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.84 Conformation dependent library (CDL) restraints added in 447.2 milliseconds 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 4 helices and 1 sheets defined 14.1% alpha, 7.6% beta 174 base pairs and 273 stacking pairs defined. Time for finding SS restraints: 7.54 Creating SS restraints... Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'D' and resid 121 through 124 No H-bonds generated for 'chain 'D' and resid 121 through 124' Processing helix chain 'v' and resid 253 through 255 No H-bonds generated for 'chain 'v' and resid 253 through 255' Processing helix chain 'v' and resid 280 through 295 Processing sheet with id= A, first strand: chain 'v' and resid 239 through 244 24 hydrogen bonds defined for protein. 66 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 444 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 273 stacking parallelities Total time for adding SS restraints: 9.64 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1726 1.33 - 1.45: 8157 1.45 - 1.57: 5781 1.57 - 1.69: 1283 1.69 - 1.81: 11 Bond restraints: 16958 Sorted by residual: bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.635 1.344 0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" N1 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.635 1.346 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C5 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.155 1.397 -0.242 2.00e-02 2.50e+03 1.47e+02 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 94.08 - 102.59: 1174 102.59 - 111.11: 9982 111.11 - 119.63: 7739 119.63 - 128.14: 6238 128.14 - 136.66: 959 Bond angle restraints: 26092 Sorted by residual: angle pdb=" O2' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" C1' G7M A2069 " ideal model delta sigma weight residual 108.40 128.85 -20.45 1.50e+00 4.44e-01 1.86e+02 angle pdb=" C3' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" O2' G7M A2069 " ideal model delta sigma weight residual 110.70 127.84 -17.14 1.50e+00 4.44e-01 1.31e+02 angle pdb=" C1' G7M A2069 " pdb=" N9 G7M A2069 " pdb=" C8 G7M A2069 " ideal model delta sigma weight residual 94.96 127.09 -32.13 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C4' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C1' G7M A2069 " ideal model delta sigma weight residual 109.90 99.64 10.26 1.00e+00 1.00e+00 1.05e+02 angle pdb=" C2' G7M A2069 " pdb=" C1' G7M A2069 " pdb=" N9 G7M A2069 " ideal model delta sigma weight residual 112.00 126.16 -14.16 1.50e+00 4.44e-01 8.91e+01 ... (remaining 26087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 7984 32.55 - 65.10: 513 65.10 - 97.65: 67 97.65 - 130.21: 4 130.21 - 162.76: 1 Dihedral angle restraints: 8569 sinusoidal: 8068 harmonic: 501 Sorted by residual: dihedral pdb=" O4' U A2585 " pdb=" C1' U A2585 " pdb=" N1 U A2585 " pdb=" C2 U A2585 " ideal model delta sinusoidal sigma weight residual -128.00 34.76 -162.76 1 1.70e+01 3.46e-03 6.49e+01 dihedral pdb=" C5' G A 748 " pdb=" C4' G A 748 " pdb=" C3' G A 748 " pdb=" O3' G A 748 " ideal model delta sinusoidal sigma weight residual 147.00 104.39 42.61 1 8.00e+00 1.56e-02 3.96e+01 dihedral pdb=" O4' U A 790 " pdb=" C1' U A 790 " pdb=" N1 U A 790 " pdb=" C2 U A 790 " ideal model delta sinusoidal sigma weight residual -160.00 -81.05 -78.95 1 1.50e+01 4.44e-03 3.45e+01 ... (remaining 8566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 3382 0.303 - 0.606: 10 0.606 - 0.909: 0 0.909 - 1.212: 1 1.212 - 1.514: 1 Chirality restraints: 3394 Sorted by residual: chirality pdb=" C2' G7M A2069 " pdb=" C3' G7M A2069 " pdb=" O2' G7M A2069 " pdb=" C1' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.75 -1.24 -1.51 2.00e-01 2.50e+01 5.73e+01 chirality pdb=" C1' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C2' G7M A2069 " pdb=" N9 G7M A2069 " both_signs ideal model delta sigma weight residual False 2.46 1.51 0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C4' G7M A2069 " pdb=" C5' G7M A2069 " pdb=" O4' G7M A2069 " pdb=" C3' G7M A2069 " both_signs ideal model delta sigma weight residual False -2.50 -1.94 -0.56 2.00e-01 2.50e+01 7.87e+00 ... (remaining 3391 not shown) Planarity restraints: 911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " 0.036 2.00e-02 2.50e+03 6.06e-01 8.28e+03 pdb=" C4' OMC A2498 " -0.480 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " -0.787 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " 0.553 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " 0.603 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " 0.206 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " -0.885 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " -0.208 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " 0.961 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.025 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' OMG A2251 " -0.470 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " -0.752 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " 0.572 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " 0.579 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " 0.212 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " -0.848 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " -0.229 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " 0.910 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " 0.112 2.00e-02 2.50e+03 5.86e-01 7.72e+03 pdb=" C4' 2MG A2445 " -0.514 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.864 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.514 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.483 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.271 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.724 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.234 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.956 2.00e-02 2.50e+03 ... (remaining 908 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 83 2.51 - 3.11: 9765 3.11 - 3.71: 33488 3.71 - 4.30: 46469 4.30 - 4.90: 56548 Nonbonded interactions: 146353 Sorted by model distance: nonbonded pdb=" OP2 A A2518 " pdb="MG MG A3021 " model vdw 1.913 2.170 nonbonded pdb=" OP2 C A 740 " pdb="MG MG A3002 " model vdw 1.915 2.170 nonbonded pdb=" OP2 OMC A2498 " pdb="MG MG A3019 " model vdw 1.918 2.170 nonbonded pdb=" OP2 C A2499 " pdb="MG MG A3019 " model vdw 1.946 2.170 nonbonded pdb=" OP2 U A 963 " pdb="MG MG A3005 " model vdw 1.948 2.170 ... (remaining 146348 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: 6 Type Number sf(0) Gaussians P 647 5.49 5 Mg 34 5.21 5 S 6 5.16 5 C 7066 2.51 5 N 2808 2.21 5 O 4765 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: 3.160 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: 13.580 Check model and map are aligned: 0.230 Process input model: 53.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.312 16958 Z= 0.600 Angle : 1.199 32.134 26092 Z= 0.762 Chirality : 0.108 1.514 3394 Planarity : 0.048 0.606 911 Dihedral : 16.630 162.758 8249 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 6.80 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.55), residues: 171 helix: -0.18 (0.90), residues: 28 sheet: -1.46 (1.10), residues: 15 loop : -2.33 (0.48), residues: 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 19 time to evaluate : 0.599 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 29 average time/residue: 0.5387 time to fit residues: 19.9907 Evaluate side-chains 18 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1326 time to fit residues: 0.6967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D 140 HIS D 148 GLN X 12 ASN ** v 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 273 GLN v 281 HIS v 283 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 16958 Z= 0.162 Angle : 0.819 15.925 26092 Z= 0.469 Chirality : 0.034 0.450 3394 Planarity : 0.011 0.124 911 Dihedral : 15.476 167.790 7898 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.04 % 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: -1.75 (0.62), residues: 171 helix: 2.78 (1.23), residues: 24 sheet: -1.99 (0.97), residues: 20 loop : -1.98 (0.50), residues: 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.596 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.3772 time to fit residues: 10.4432 Evaluate side-chains 19 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1573 time to fit residues: 1.0131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 GLN ** v 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.059 16958 Z= 0.513 Angle : 0.966 13.697 26092 Z= 0.522 Chirality : 0.046 0.470 3394 Planarity : 0.013 0.139 911 Dihedral : 15.379 155.878 7898 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 5.44 % 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: -1.93 (0.59), residues: 171 helix: 1.51 (1.06), residues: 24 sheet: -1.62 (1.11), residues: 20 loop : -1.94 (0.50), residues: 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 15 time to evaluate : 0.599 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 20 average time/residue: 0.4657 time to fit residues: 12.8283 Evaluate side-chains 20 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3179 time to fit residues: 2.6813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.8521 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 16958 Z= 0.378 Angle : 0.874 13.925 26092 Z= 0.486 Chirality : 0.040 0.431 3394 Planarity : 0.012 0.133 911 Dihedral : 15.221 154.731 7898 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.58), residues: 171 helix: 0.67 (0.97), residues: 24 sheet: -1.49 (1.10), residues: 20 loop : -1.90 (0.50), residues: 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.577 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.4619 time to fit residues: 11.4368 Evaluate side-chains 17 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4742 time to fit residues: 1.0580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.8539 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 16958 Z= 0.425 Angle : 0.908 14.338 26092 Z= 0.499 Chirality : 0.042 0.461 3394 Planarity : 0.012 0.136 911 Dihedral : 15.245 151.425 7898 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.58), residues: 171 helix: 0.39 (1.05), residues: 24 sheet: -1.49 (1.12), residues: 20 loop : -1.86 (0.49), residues: 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.642 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.4737 time to fit residues: 11.0988 Evaluate side-chains 18 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3473 time to fit residues: 1.3758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 16958 Z= 0.293 Angle : 0.830 14.477 26092 Z= 0.467 Chirality : 0.036 0.428 3394 Planarity : 0.012 0.129 911 Dihedral : 15.091 163.178 7898 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -1.98 (0.59), residues: 171 helix: 0.78 (1.08), residues: 24 sheet: -1.59 (1.13), residues: 20 loop : -1.83 (0.49), residues: 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.628 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.4721 time to fit residues: 9.8844 Evaluate side-chains 15 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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: 0.8550 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.056 16958 Z= 0.488 Angle : 0.940 14.273 26092 Z= 0.510 Chirality : 0.044 0.460 3394 Planarity : 0.013 0.136 911 Dihedral : 15.254 155.136 7898 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.58), residues: 171 helix: 0.18 (1.09), residues: 24 sheet: -1.75 (1.13), residues: 20 loop : -1.89 (0.49), residues: 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.547 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.5144 time to fit residues: 12.3042 Evaluate side-chains 19 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2551 time to fit residues: 1.6003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.8517 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 16958 Z= 0.380 Angle : 0.878 14.451 26092 Z= 0.486 Chirality : 0.040 0.447 3394 Planarity : 0.012 0.133 911 Dihedral : 15.144 146.595 7898 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -2.23 (0.58), residues: 171 helix: 0.00 (1.09), residues: 24 sheet: -1.73 (1.15), residues: 20 loop : -1.88 (0.49), residues: 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.634 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.4388 time to fit residues: 9.9259 Evaluate side-chains 16 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8550 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.052 16958 Z= 0.488 Angle : 0.938 14.374 26092 Z= 0.510 Chirality : 0.044 0.452 3394 Planarity : 0.013 0.138 911 Dihedral : 15.214 144.859 7898 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % 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: -2.33 (0.58), residues: 171 helix: -0.15 (1.11), residues: 24 sheet: -1.77 (1.15), residues: 20 loop : -1.94 (0.49), residues: 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.580 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.4455 time to fit residues: 9.9397 Evaluate side-chains 16 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8496 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 16958 Z= 0.316 Angle : 0.845 14.491 26092 Z= 0.473 Chirality : 0.037 0.438 3394 Planarity : 0.012 0.130 911 Dihedral : 15.068 144.750 7898 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.58), residues: 171 helix: 0.02 (1.11), residues: 24 sheet: -1.78 (1.14), residues: 20 loop : -1.85 (0.49), residues: 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.556 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.4542 time to fit residues: 10.0771 Evaluate side-chains 17 residues out of total 147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1551 time to fit residues: 0.7151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.119813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.108773 restraints weight = 22923.118| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 0.59 r_work: 0.3065 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.046 16958 Z= 0.446 Angle : 0.910 14.383 26092 Z= 0.498 Chirality : 0.042 0.438 3394 Planarity : 0.012 0.136 911 Dihedral : 15.128 143.408 7898 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.58), residues: 171 helix: -0.05 (1.12), residues: 24 sheet: -1.77 (1.14), residues: 20 loop : -1.93 (0.48), residues: 127 =============================================================================== Job complete usr+sys time: 1844.08 seconds wall clock time: 35 minutes 17.94 seconds (2117.94 seconds total)