Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:25:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/04_2023/8eqj_28538_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/04_2023/8eqj_28538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/04_2023/8eqj_28538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/04_2023/8eqj_28538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/04_2023/8eqj_28538_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqj_28538/04_2023/8eqj_28538_neut_updated.pdb" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 16 5.16 5 C 2140 2.51 5 N 492 2.21 5 O 580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3232 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1571 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 1 Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1571 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 57 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 57 Time building chain proxies: 2.33, per 1000 atoms: 0.72 Number of scatterers: 3232 At special positions: 0 Unit cell: (64.988, 61.612, 91.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 4 15.00 O 580 8.00 N 492 7.00 C 2140 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: 1.28 Conformation dependent library (CDL) restraints added in 436.0 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 4 sheets defined 45.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.592A pdb=" N LYS A 61 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 99 Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'B' and resid 44 through 61 removed outlier: 3.591A pdb=" N LYS B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 99 Processing helix chain 'B' and resid 106 through 133 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.922A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 229 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= C, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.922A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 229 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 186 186 hydrogen bonds defined for protein. 534 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: 0.88 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 470 1.31 - 1.43: 1028 1.43 - 1.56: 1798 1.56 - 1.68: 8 1.68 - 1.81: 18 Bond restraints: 3322 Sorted by residual: bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C30 PEE B 402 " pdb=" O3 PEE B 402 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C30 PEE A 402 " pdb=" O3 PEE A 402 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C10 PEE B 402 " pdb=" O2 PEE B 402 " ideal model delta sigma weight residual 1.332 1.403 -0.071 2.00e-02 2.50e+03 1.24e+01 ... (remaining 3317 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.53: 92 107.53 - 114.18: 1906 114.18 - 120.83: 1481 120.83 - 127.48: 999 127.48 - 134.13: 42 Bond angle restraints: 4520 Sorted by residual: angle pdb=" O3P PEE B 402 " pdb=" P PEE B 402 " pdb=" O4P PEE B 402 " ideal model delta sigma weight residual 92.91 109.79 -16.88 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O3P PEE A 402 " pdb=" P PEE A 402 " pdb=" O4P PEE A 402 " ideal model delta sigma weight residual 92.91 109.79 -16.88 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.75 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.74 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" O1P PEE A 402 " pdb=" P PEE A 402 " pdb=" O2P PEE A 402 " ideal model delta sigma weight residual 119.43 109.11 10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 4515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.13: 1791 31.13 - 62.25: 41 62.25 - 93.38: 12 93.38 - 124.51: 8 124.51 - 155.63: 6 Dihedral angle restraints: 1858 sinusoidal: 714 harmonic: 1144 Sorted by residual: dihedral pdb=" N PEE B 401 " pdb=" C4 PEE B 401 " pdb=" C5 PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sinusoidal sigma weight residual 303.03 147.40 155.63 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" N PEE A 401 " pdb=" C4 PEE A 401 " pdb=" C5 PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sinusoidal sigma weight residual 303.03 147.41 155.62 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" N PEE A 402 " pdb=" C4 PEE A 402 " pdb=" C5 PEE A 402 " pdb=" O4P PEE A 402 " ideal model delta sinusoidal sigma weight residual 303.03 151.71 151.32 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 1855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 362 0.037 - 0.073: 100 0.073 - 0.110: 36 0.110 - 0.146: 2 0.146 - 0.183: 6 Chirality restraints: 506 Sorted by residual: chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" C2 PEE B 402 " pdb=" C1 PEE B 402 " pdb=" C3 PEE B 402 " pdb=" O2 PEE B 402 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 503 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 87 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C PHE A 87 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE A 87 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 88 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 87 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C PHE B 87 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE B 87 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 88 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 84 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C LEU B 84 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU B 84 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 85 " -0.009 2.00e-02 2.50e+03 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 443 2.75 - 3.29: 3213 3.29 - 3.83: 5449 3.83 - 4.36: 6110 4.36 - 4.90: 10718 Nonbonded interactions: 25933 Sorted by model distance: nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.219 2.440 nonbonded pdb=" OG1 THR B 151 " pdb=" O TYR B 154 " model vdw 2.219 2.440 nonbonded pdb=" OG SER A 205 " pdb=" O THR A 208 " model vdw 2.286 2.440 nonbonded pdb=" OG SER B 205 " pdb=" O THR B 208 " model vdw 2.287 2.440 nonbonded pdb=" ND2 ASN B 137 " pdb=" O CYS B 157 " model vdw 2.309 2.520 ... (remaining 25928 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.550 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.620 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 0.005 0.071 3322 Z= 0.326 Angle : 0.940 16.875 4520 Z= 0.385 Chirality : 0.043 0.183 506 Planarity : 0.005 0.029 534 Dihedral : 20.599 155.632 1126 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -0.19 (0.41), residues: 376 helix: 0.56 (0.38), residues: 174 sheet: 0.33 (0.51), residues: 88 loop : -1.44 (0.51), residues: 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.5475 time to fit residues: 57.9375 Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.7064 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3322 Z= 0.215 Angle : 0.513 7.702 4520 Z= 0.255 Chirality : 0.040 0.129 506 Planarity : 0.004 0.027 534 Dihedral : 19.641 137.755 450 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.86 % 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: 1.42 (0.41), residues: 376 helix: 2.54 (0.37), residues: 176 sheet: 0.35 (0.54), residues: 84 loop : -1.17 (0.49), residues: 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.368 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 58 average time/residue: 0.8801 time to fit residues: 53.0564 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 3322 Z= 0.319 Angle : 0.516 5.331 4520 Z= 0.271 Chirality : 0.040 0.136 506 Planarity : 0.004 0.031 534 Dihedral : 15.038 118.859 450 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 4.02 % 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: 1.51 (0.43), residues: 376 helix: 2.82 (0.37), residues: 176 sheet: -0.15 (0.53), residues: 88 loop : -1.05 (0.52), residues: 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.366 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 64 average time/residue: 0.8358 time to fit residues: 55.7066 Evaluate side-chains 64 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.0331 time to fit residues: 0.5968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3322 Z= 0.245 Angle : 0.477 4.635 4520 Z= 0.251 Chirality : 0.039 0.125 506 Planarity : 0.003 0.031 534 Dihedral : 12.537 118.053 450 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 2.30 % 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: 1.41 (0.42), residues: 376 helix: 2.81 (0.37), residues: 176 sheet: -0.52 (0.53), residues: 84 loop : -0.90 (0.52), residues: 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.377 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.8465 time to fit residues: 52.9129 Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0333 time to fit residues: 0.6163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7146 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3322 Z= 0.230 Angle : 0.453 4.346 4520 Z= 0.240 Chirality : 0.039 0.125 506 Planarity : 0.003 0.031 534 Dihedral : 11.843 118.351 450 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 2.59 % 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: 1.27 (0.42), residues: 376 helix: 2.72 (0.37), residues: 176 sheet: -0.60 (0.52), residues: 84 loop : -1.01 (0.50), residues: 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.368 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.7565 time to fit residues: 49.1033 Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0329 time to fit residues: 0.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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: 0.7125 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 3322 Z= 0.156 Angle : 0.425 4.835 4520 Z= 0.226 Chirality : 0.039 0.123 506 Planarity : 0.003 0.029 534 Dihedral : 10.759 116.472 450 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 0.86 % 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: 1.37 (0.42), residues: 376 helix: 2.80 (0.37), residues: 176 sheet: -0.55 (0.52), residues: 84 loop : -0.95 (0.49), residues: 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.370 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.6566 time to fit residues: 37.4418 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.0060 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.7143 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3322 Z= 0.199 Angle : 0.436 5.974 4520 Z= 0.231 Chirality : 0.039 0.138 506 Planarity : 0.003 0.029 534 Dihedral : 10.171 115.719 450 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 1.72 % 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: 1.38 (0.42), residues: 376 helix: 2.84 (0.37), residues: 176 sheet: -0.65 (0.53), residues: 84 loop : -0.91 (0.49), residues: 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.335 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.8127 time to fit residues: 47.4776 Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.4922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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: 0.7149 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3322 Z= 0.223 Angle : 0.463 7.532 4520 Z= 0.241 Chirality : 0.040 0.127 506 Planarity : 0.003 0.029 534 Dihedral : 9.915 115.463 450 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 2.87 % 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: 1.27 (0.42), residues: 376 helix: 2.75 (0.37), residues: 176 sheet: -0.70 (0.52), residues: 84 loop : -0.96 (0.49), residues: 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.381 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.7572 time to fit residues: 44.4729 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.7155 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 3322 Z= 0.228 Angle : 0.469 7.863 4520 Z= 0.243 Chirality : 0.040 0.119 506 Planarity : 0.003 0.031 534 Dihedral : 9.699 115.479 450 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 2.01 % 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: 1.19 (0.42), residues: 376 helix: 2.70 (0.37), residues: 176 sheet: -0.74 (0.52), residues: 84 loop : -1.03 (0.49), residues: 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.381 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.8596 time to fit residues: 48.4191 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.7154 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3322 Z= 0.227 Angle : 0.471 7.305 4520 Z= 0.246 Chirality : 0.040 0.120 506 Planarity : 0.003 0.030 534 Dihedral : 9.690 115.469 450 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 1.72 % 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: 1.57 (0.43), residues: 376 helix: 3.18 (0.37), residues: 164 sheet: -0.74 (0.52), residues: 84 loop : -0.56 (0.53), residues: 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.372 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 56 average time/residue: 0.8661 time to fit residues: 50.6082 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.0170 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.131356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099468 restraints weight = 3673.180| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.38 r_work: 0.2837 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3322 Z= 0.193 Angle : 0.472 7.266 4520 Z= 0.247 Chirality : 0.040 0.119 506 Planarity : 0.003 0.030 534 Dihedral : 9.584 115.952 450 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 2.01 % 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: 1.31 (0.42), residues: 376 helix: 2.78 (0.37), residues: 176 sheet: -0.70 (0.52), residues: 84 loop : -0.92 (0.50), residues: 116 =============================================================================== Job complete usr+sys time: 1623.61 seconds wall clock time: 29 minutes 47.31 seconds (1787.31 seconds total)