Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 10:27:38 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/01_2021/6riu_4898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/01_2021/6riu_4898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/01_2021/6riu_4898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/01_2021/6riu_4898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/01_2021/6riu_4898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/01_2021/6riu_4898.pdb" } resolution = 3.9 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= 0.001 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 2882 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "B" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Time building chain proxies: 1.86, per 1000 atoms: 0.65 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Number of scatterers: 2882 At special positions: 0 Unit cell: (69.828, 47.61, 49.726, 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 4 16.00 O 278 8.00 N 250 7.00 C 920 6.00 H 1430 1.00 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 Amimo 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: 2.75 Conformation dependent library (CDL) restraints added in 256.3 milliseconds 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 340 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 3.553A pdb=" N LYS A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.757A pdb=" N ALA A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.553A pdb=" N LYS B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.758A pdb=" N ALA B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Proline residue: B 77 - end of helix No H-bonds generated for 'chain 'B' and resid 74 through 79' Processing helix chain 'B' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1430 1.03 - 1.22: 3 1.22 - 1.42: 616 1.42 - 1.61: 853 1.61 - 1.80: 8 Bond restraints: 2910 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.95e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.83e+00 bond pdb=" N LEU B 83 " pdb=" CA LEU B 83 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.23e-02 6.61e+03 7.01e+00 bond pdb=" N LEU A 83 " pdb=" CA LEU A 83 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N LEU B 83 " pdb=" H LEU B 83 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.42e+00 ... (remaining 2905 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.51: 49 105.51 - 112.62: 3274 112.62 - 119.74: 854 119.74 - 126.86: 1054 126.86 - 133.97: 23 Bond angle restraints: 5254 Sorted by residual: angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 112.49 103.08 9.41 1.21e+00 6.83e-01 6.04e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 112.49 103.14 9.35 1.21e+00 6.83e-01 5.97e+01 angle pdb=" N LYS B 9 " pdb=" CA LYS B 9 " pdb=" C LYS B 9 " ideal model delta sigma weight residual 112.89 106.94 5.95 1.24e+00 6.50e-01 2.30e+01 angle pdb=" N GLU B 36 " pdb=" CA GLU B 36 " pdb=" C GLU B 36 " ideal model delta sigma weight residual 110.58 117.63 -7.05 1.56e+00 4.11e-01 2.04e+01 angle pdb=" N VAL B 35 " pdb=" CA VAL B 35 " pdb=" C VAL B 35 " ideal model delta sigma weight residual 111.45 115.61 -4.16 9.30e-01 1.16e+00 2.01e+01 ... (remaining 5249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 1071 17.93 - 35.87: 63 35.87 - 53.80: 16 53.80 - 71.74: 2 71.74 - 89.67: 6 Dihedral angle restraints: 1158 sinusoidal: 546 harmonic: 612 Sorted by residual: dihedral pdb=" CA LEU A 74 " pdb=" C LEU A 74 " pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU B 74 " pdb=" C LEU B 74 " pdb=" N SER B 75 " pdb=" CA SER B 75 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU A 56 " pdb=" C LEU A 56 " pdb=" N ASP A 57 " pdb=" CA ASP A 57 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 214 0.153 - 0.306: 4 0.306 - 0.459: 0 0.459 - 0.612: 0 0.612 - 0.765: 2 Chirality restraints: 220 Sorted by residual: chirality pdb=" CG LEU A 74 " pdb=" CB LEU A 74 " pdb=" CD1 LEU A 74 " pdb=" CD2 LEU A 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CG LEU B 74 " pdb=" CB LEU B 74 " pdb=" CD1 LEU B 74 " pdb=" CD2 LEU B 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA ALA A 34 " pdb=" N ALA A 34 " pdb=" C ALA A 34 " pdb=" CB ALA A 34 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 217 not shown) Planarity restraints: 434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 59 " -0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C MET B 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET B 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA B 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 59 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C MET A 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET A 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 76 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 77 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.045 5.00e-02 4.00e+02 ... (remaining 431 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 34 2.00 - 2.65: 4114 2.65 - 3.30: 8622 3.30 - 3.95: 10370 3.95 - 4.60: 15836 Nonbonded interactions: 38976 Sorted by model distance: nonbonded pdb=" OG SER A 75 " pdb=" HG SER B 75 " model vdw 1.355 1.850 nonbonded pdb=" O GLY B 30 " pdb=" HG SER B 33 " model vdw 1.488 1.850 nonbonded pdb=" O GLY A 30 " pdb=" HG SER A 33 " model vdw 1.520 1.850 nonbonded pdb=" OD1 ASP B 49 " pdb=" HH TYR B 64 " model vdw 1.659 1.850 nonbonded pdb=" O ILE A 87 " pdb=" HG1 THR A 91 " model vdw 1.713 1.850 ... (remaining 38971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 1452 2882 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 4 5.16 5 C 920 2.51 5 N 250 2.21 5 O 278 1.98 5 H 1430 0.53 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 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: 2.300 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.240 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.020 Process input model: 16.620 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.320 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.068 1480 Angle : 1.188 9.406 2006 Chirality : 0.089 0.765 220 Planarity : 0.011 0.081 260 Dihedral : 15.190 89.671 546 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % 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: -5.77 (0.42), residues: 178 helix: -3.50 (0.29), residues: 134 sheet: None (None), residues: 0 loop : -4.10 (0.72), residues: 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.3867 time to fit residues: 13.5650 Evaluate side-chains 17 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.6843 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.019 1480 Angle : 0.625 5.161 2006 Chirality : 0.040 0.162 220 Planarity : 0.007 0.057 260 Dihedral : 6.051 21.225 196 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -4.14 (0.53), residues: 178 helix: -2.30 (0.38), residues: 138 sheet: None (None), residues: 0 loop : -3.63 (0.81), residues: 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2650 time to fit residues: 5.4110 Evaluate side-chains 17 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.017 1480 Angle : 0.550 3.683 2006 Chirality : 0.036 0.105 220 Planarity : 0.005 0.035 260 Dihedral : 5.377 18.747 196 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -3.44 (0.57), residues: 178 helix: -1.76 (0.38), residues: 148 sheet: None (None), residues: 0 loop : -3.90 (1.09), residues: 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2507 time to fit residues: 5.1416 Evaluate side-chains 17 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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: 0.6790 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.015 1480 Angle : 0.536 3.665 2006 Chirality : 0.035 0.104 220 Planarity : 0.004 0.035 260 Dihedral : 5.026 15.812 196 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -2.98 (0.57), residues: 178 helix: -1.69 (0.36), residues: 164 sheet: None (None), residues: 0 loop : -2.29 (2.05), residues: 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.3181 time to fit residues: 7.0930 Evaluate side-chains 13 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.0070 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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: 0.6748 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.015 1480 Angle : 0.495 3.600 2006 Chirality : 0.034 0.105 220 Planarity : 0.005 0.053 260 Dihedral : 4.607 14.228 196 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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: -2.36 (0.60), residues: 178 helix: -1.26 (0.38), residues: 164 sheet: None (None), residues: 0 loop : -2.53 (1.88), residues: 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.3642 time to fit residues: 7.3507 Evaluate side-chains 13 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.6809 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.031 1480 Angle : 0.505 4.316 2006 Chirality : 0.035 0.119 220 Planarity : 0.004 0.032 260 Dihedral : 4.495 14.617 196 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -2.19 (0.59), residues: 178 helix: -0.88 (0.39), residues: 156 sheet: None (None), residues: 0 loop : -4.54 (1.16), residues: 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.356 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.3536 time to fit residues: 7.1344 Evaluate side-chains 14 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.7636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.018 1480 Angle : 0.537 4.136 2006 Chirality : 0.035 0.118 220 Planarity : 0.004 0.031 260 Dihedral : 4.336 13.330 196 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: -1.06 (0.62), residues: 178 helix: -0.13 (0.41), residues: 154 sheet: None (None), residues: 0 loop : -3.80 (1.16), residues: 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3267 time to fit residues: 5.6842 Evaluate side-chains 11 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.7939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.015 1480 Angle : 0.504 3.711 2006 Chirality : 0.034 0.112 220 Planarity : 0.003 0.032 260 Dihedral : 4.132 12.665 196 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % 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: -0.47 (0.64), residues: 178 helix: 0.28 (0.42), residues: 154 sheet: None (None), residues: 0 loop : -3.72 (1.17), residues: 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3236 time to fit residues: 5.5946 Evaluate side-chains 11 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.0470 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.8211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.013 1480 Angle : 0.485 3.652 2006 Chirality : 0.033 0.101 220 Planarity : 0.003 0.033 260 Dihedral : 3.902 11.215 196 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -0.02 (0.65), residues: 178 helix: 0.59 (0.43), residues: 154 sheet: None (None), residues: 0 loop : -3.66 (1.19), residues: 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.3269 time to fit residues: 4.9843 Evaluate side-chains 11 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.8355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.014 1480 Angle : 0.489 3.789 2006 Chirality : 0.033 0.102 220 Planarity : 0.003 0.033 260 Dihedral : 3.922 11.670 196 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: 0.10 (0.66), residues: 178 helix: 0.65 (0.43), residues: 154 sheet: None (None), residues: 0 loop : -3.40 (1.27), residues: 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield and 0 Emsley and 178 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.320 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.3183 time to fit residues: 5.1819 Evaluate side-chains 12 residues out of total 152 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.134999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.118057 restraints weight = 30101.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.121418 restraints weight = 18697.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.124005 restraints weight = 12719.967| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.029 1480 ANGLE : 0.522 5.460 2006 CHIRALITY : 0.033 0.101 220 PLANARITY : 0.003 0.034 260 DIHEDRAL : 3.895 10.981 196 MIN NONBONDED DISTANCE : 1.969 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 13.17 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.49 % FAVORED : 95.51 % 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: 0.20 (0.66), RESIDUES: 178 HELIX: 0.71 (0.43), RESIDUES: 154 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -3.30 (1.34), RESIDUES: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.8507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.029 1480 Angle : 0.522 5.460 2006 Chirality : 0.033 0.101 220 Planarity : 0.003 0.034 260 Dihedral : 3.895 10.981 196 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: 0.20 (0.66), residues: 178 helix: 0.71 (0.43), residues: 154 sheet: None (None), residues: 0 loop : -3.30 (1.34), residues: 24 =============================================================================== Job complete usr+sys time: 2019.86 seconds wall clock time: 36 minutes 0.58 seconds (2160.58 seconds total)