Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:35:56 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlk_22246/12_2021/6xlk_22246_updated.pdb" } resolution = 3.3 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= 0.004 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-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 5456 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 255, 'PCIS': 1} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 255, 'PCIS': 1} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'1N7': 1, '118': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'1N7': 1, '118': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.58, per 1000 atoms: 0.66 Number of scatterers: 5456 At special positions: 0 Unit cell: (86.645, 115.971, 87.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sb 2 50.95 S 26 16.00 P 44 15.00 O 1086 8.00 N 912 7.00 C 3386 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 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: 2.45 Conformation dependent library (CDL) restraints added in 652.1 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 41.2% alpha, 19.8% beta 23 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'G' and resid 4 through 11 Processing helix chain 'G' and resid 15 through 23 Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.941A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 108 Processing helix chain 'G' and resid 136 through 141 removed outlier: 3.952A pdb=" N LYS G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 153 removed outlier: 3.633A pdb=" N MET G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 232 removed outlier: 4.799A pdb=" N ARG G 220 " --> pdb=" O ASP G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 10 Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 43 through 58 removed outlier: 3.540A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 108 removed outlier: 3.551A pdb=" N ARG H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 153 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 216 through 232 removed outlier: 4.960A pdb=" N ARG H 220 " --> pdb=" O ASP H 217 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN H 221 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP H 232 " --> pdb=" O TRP H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'G' and resid 117 through 121 removed outlier: 6.703A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 235 through 237 Processing sheet with id= C, first strand: chain 'H' and resid 117 through 121 removed outlier: 6.403A pdb=" N GLU H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR H 245 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN H 263 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU H 243 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 235 through 237 222 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 2323 1.39 - 1.58: 3224 1.58 - 1.76: 88 1.76 - 1.95: 42 1.95 - 2.13: 8 Bond restraints: 5685 Sorted by residual: bond pdb=" C17 1N7 G 301 " pdb=" O3 1N7 G 301 " ideal model delta sigma weight residual 0.000 1.396 -1.396 2.00e-02 2.50e+03 4.87e+03 bond pdb=" C17 1N7 H 301 " pdb=" O3 1N7 H 301 " ideal model delta sigma weight residual 0.000 1.395 -1.395 2.00e-02 2.50e+03 4.87e+03 bond pdb=" C18 1N7 H 301 " pdb=" C6 1N7 H 301 " ideal model delta sigma weight residual 0.987 1.513 -0.526 2.00e-02 2.50e+03 6.93e+02 bond pdb=" C18 1N7 G 301 " pdb=" C6 1N7 G 301 " ideal model delta sigma weight residual 0.987 1.513 -0.526 2.00e-02 2.50e+03 6.91e+02 bond pdb=" C17 1N7 G 301 " pdb=" C18 1N7 G 301 " ideal model delta sigma weight residual 1.147 1.535 -0.388 2.00e-02 2.50e+03 3.76e+02 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 431 106.47 - 113.36: 3098 113.36 - 120.24: 2179 120.24 - 127.13: 2063 127.13 - 134.02: 137 Bond angle restraints: 7908 Sorted by residual: angle pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sigma weight residual 120.20 124.66 -4.46 1.50e+00 4.44e-01 8.85e+00 angle pdb=" N PRO H 144 " pdb=" CA PRO H 144 " pdb=" C PRO H 144 " ideal model delta sigma weight residual 110.70 113.79 -3.09 1.22e+00 6.72e-01 6.44e+00 angle pdb=" CA TYR H 127 " pdb=" CB TYR H 127 " pdb=" CG TYR H 127 " ideal model delta sigma weight residual 113.90 118.39 -4.49 1.80e+00 3.09e-01 6.22e+00 angle pdb=" C4' DG T 40 " pdb=" O4' DG T 40 " pdb=" C1' DG T 40 " ideal model delta sigma weight residual 109.70 105.97 3.73 1.50e+00 4.44e-01 6.17e+00 angle pdb=" C THR G 206 " pdb=" CA THR G 206 " pdb=" CB THR G 206 " ideal model delta sigma weight residual 109.80 113.58 -3.78 1.64e+00 3.72e-01 5.31e+00 ... (remaining 7903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.85: 2933 31.85 - 63.70: 254 63.70 - 95.54: 13 95.54 - 127.39: 0 127.39 - 159.24: 1 Dihedral angle restraints: 3201 sinusoidal: 1605 harmonic: 1596 Sorted by residual: dihedral pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sinusoidal sigma weight residual 220.00 60.76 159.24 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA VAL H 126 " pdb=" C VAL H 126 " pdb=" N TYR H 127 " pdb=" CA TYR H 127 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR G 114 " pdb=" C TYR G 114 " pdb=" N GLN G 115 " pdb=" CA GLN G 115 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 3198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 864 0.286 - 0.572: 6 0.572 - 0.858: 2 0.858 - 1.144: 0 1.144 - 1.429: 2 Chirality restraints: 874 Sorted by residual: chirality pdb=" C18 1N7 G 301 " pdb=" C17 1N7 G 301 " pdb=" C19 1N7 G 301 " pdb=" C6 1N7 G 301 " both_signs ideal model delta sigma weight residual False 1.21 2.64 -1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" C18 1N7 H 301 " pdb=" C17 1N7 H 301 " pdb=" C19 1N7 H 301 " pdb=" C6 1N7 H 301 " both_signs ideal model delta sigma weight residual False 1.21 2.64 -1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" C6 1N7 H 301 " pdb=" C18 1N7 H 301 " pdb=" C5 1N7 H 301 " pdb=" C7 1N7 H 301 " both_signs ideal model delta sigma weight residual False -1.78 -2.63 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 871 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO G 144 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO G 145 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 145 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 145 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 224 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ILE G 224 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE G 224 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR G 225 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 206 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C THR G 206 " 0.026 2.00e-02 2.50e+03 pdb=" O THR G 206 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA G 207 " -0.009 2.00e-02 2.50e+03 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 833 2.75 - 3.29: 5125 3.29 - 3.83: 9686 3.83 - 4.36: 11493 4.36 - 4.90: 18303 Nonbonded interactions: 45440 Sorted by model distance: nonbonded pdb=" NE2 HIS G 170 " pdb=" OE1 GLU G 182 " model vdw 2.216 2.520 nonbonded pdb=" OG1 THR G 61 " pdb=" OE1 GLU G 64 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR G 139 " pdb=" OG1 THR G 167 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR G 127 " pdb=" OE1 GLU G 185 " model vdw 2.250 2.440 nonbonded pdb=" OG SER H 2 " pdb=" O TYR H 41 " model vdw 2.266 2.440 ... (remaining 45435 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 'G' selection = (chain 'H' and (resid 2 through 269 or (resid 301 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 )) or resid 302)) } ncs_group { reference = (chain 'N' and (resid 41 through 50 or resid 52 through 61)) selection = (chain 'T' and (resid 28 through 37 or resid 39 through 48)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Sb 2 10.97 5 P 44 5.49 5 S 26 5.16 5 C 3386 2.51 5 N 912 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Write .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: 0.880 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: 4.040 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 20.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.090 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.033 1.396 5685 Z= 1.570 Angle : 0.785 7.684 7908 Z= 0.430 Chirality : 0.099 1.429 874 Planarity : 0.004 0.057 832 Dihedral : 20.174 159.238 2173 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.26 (0.31), residues: 532 helix: -0.90 (0.30), residues: 222 sheet: -2.49 (0.42), residues: 102 loop : -1.40 (0.38), residues: 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.591 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.2608 time to fit residues: 17.7794 Evaluate side-chains 38 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0512 time to fit residues: 0.8805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 50 optimal weight: 0.0970 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 ASN G 45 GLN G 51 GLN G 76 HIS G 105 HIS G 148 GLN H 3 GLN H 50 HIS H 88 GLN H 105 HIS H 154 ASN H 193 ASN ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 5685 Z= 0.280 Angle : 0.693 9.169 7908 Z= 0.365 Chirality : 0.044 0.306 874 Planarity : 0.005 0.057 832 Dihedral : 22.360 158.953 1059 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.65 (0.33), residues: 532 helix: -0.35 (0.32), residues: 222 sheet: -2.47 (0.44), residues: 92 loop : -1.05 (0.38), residues: 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.594 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.1495 time to fit residues: 9.0966 Evaluate side-chains 40 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0550 time to fit residues: 1.2473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 40 optimal weight: 0.0170 chunk 38 optimal weight: 0.7980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 5685 Z= 0.280 Angle : 0.693 9.159 7908 Z= 0.365 Chirality : 0.044 0.306 874 Planarity : 0.005 0.057 832 Dihedral : 22.360 158.953 1059 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.65 (0.33), residues: 532 helix: -0.35 (0.32), residues: 222 sheet: -2.47 (0.44), residues: 92 loop : -1.05 (0.38), residues: 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.601 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1504 time to fit residues: 8.3446 Evaluate side-chains 35 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0613 time to fit residues: 0.7824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.173 5685 Z= 0.359 Angle : 0.653 8.187 7908 Z= 0.350 Chirality : 0.043 0.184 874 Planarity : 0.004 0.057 832 Dihedral : 22.338 159.162 1059 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.53 (0.33), residues: 532 helix: -0.25 (0.32), residues: 222 sheet: -2.44 (0.45), residues: 92 loop : -0.96 (0.38), residues: 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.578 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 0.1454 time to fit residues: 8.0883 Evaluate side-chains 38 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0517 time to fit residues: 1.3346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.173 5685 Z= 0.359 Angle : 0.653 8.186 7908 Z= 0.349 Chirality : 0.043 0.184 874 Planarity : 0.004 0.057 832 Dihedral : 22.338 159.162 1059 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.53 (0.33), residues: 532 helix: -0.25 (0.32), residues: 222 sheet: -2.44 (0.45), residues: 92 loop : -0.96 (0.38), residues: 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.636 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1580 time to fit residues: 7.5627 Evaluate side-chains 32 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 5685 Z= 0.276 Angle : 0.633 8.502 7908 Z= 0.340 Chirality : 0.042 0.172 874 Planarity : 0.004 0.056 832 Dihedral : 22.320 159.297 1059 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.49 (0.33), residues: 532 helix: -0.20 (0.32), residues: 222 sheet: -2.44 (0.45), residues: 92 loop : -0.95 (0.38), residues: 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.570 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.1537 time to fit residues: 7.6797 Evaluate side-chains 33 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0449 time to fit residues: 0.6995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 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: 0.8367 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 5685 Z= 0.318 Angle : 0.624 8.897 7908 Z= 0.336 Chirality : 0.041 0.163 874 Planarity : 0.004 0.056 832 Dihedral : 22.307 159.357 1059 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.43 (0.33), residues: 532 helix: -0.15 (0.32), residues: 222 sheet: -2.41 (0.45), residues: 92 loop : -0.92 (0.39), residues: 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.593 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.1524 time to fit residues: 7.2518 Evaluate side-chains 33 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0601 time to fit residues: 0.7854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8367 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 5685 Z= 0.318 Angle : 0.623 8.895 7908 Z= 0.336 Chirality : 0.041 0.163 874 Planarity : 0.004 0.056 832 Dihedral : 22.307 159.357 1059 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.43 (0.33), residues: 532 helix: -0.15 (0.32), residues: 222 sheet: -2.41 (0.45), residues: 92 loop : -0.92 (0.39), residues: 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.606 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1653 time to fit residues: 7.7342 Evaluate side-chains 32 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.124 5685 Z= 0.316 Angle : 0.622 8.935 7908 Z= 0.335 Chirality : 0.041 0.164 874 Planarity : 0.004 0.056 832 Dihedral : 22.305 159.360 1059 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.43 (0.33), residues: 532 helix: -0.15 (0.32), residues: 222 sheet: -2.41 (0.45), residues: 92 loop : -0.92 (0.39), residues: 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.631 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.1570 time to fit residues: 7.5359 Evaluate side-chains 33 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0579 time to fit residues: 0.8802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 5685 Z= 0.289 Angle : 0.620 9.045 7908 Z= 0.334 Chirality : 0.041 0.166 874 Planarity : 0.004 0.056 832 Dihedral : 22.299 159.415 1059 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.40 (0.33), residues: 532 helix: -0.11 (0.33), residues: 222 sheet: -2.41 (0.45), residues: 92 loop : -0.90 (0.39), residues: 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.612 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1567 time to fit residues: 8.0490 Evaluate side-chains 33 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0521 time to fit residues: 0.8497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.101773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085802 restraints weight = 13566.530| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.24 r_work: 0.3277 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work: 0.3251 rms_B_bonded: 2.08 restraints_weight: 0.1250 r_work: 0.3237 rms_B_bonded: 2.20 restraints_weight: 0.0625 r_work: 0.3223 rms_B_bonded: 2.37 restraints_weight: 0.0312 r_work: 0.3208 rms_B_bonded: 2.59 restraints_weight: 0.0156 r_work: 0.3191 rms_B_bonded: 2.84 restraints_weight: 0.0078 r_work: 0.3174 rms_B_bonded: 3.15 restraints_weight: 0.0039 r_work: 0.3155 rms_B_bonded: 3.50 restraints_weight: 0.0020 r_work: 0.3135 rms_B_bonded: 3.90 restraints_weight: 0.0010 r_work: 0.3113 rms_B_bonded: 4.37 restraints_weight: 0.0005 r_work: 0.3088 rms_B_bonded: 4.90 restraints_weight: 0.0002 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 5685 Z= 0.289 Angle : 0.619 9.031 7908 Z= 0.334 Chirality : 0.041 0.165 874 Planarity : 0.004 0.056 832 Dihedral : 22.298 159.415 1059 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.40 (0.33), residues: 532 helix: -0.11 (0.33), residues: 222 sheet: -2.41 (0.45), residues: 92 loop : -0.90 (0.39), residues: 218 =============================================================================== Job complete usr+sys time: 1153.09 seconds wall clock time: 21 minutes 45.17 seconds (1305.17 seconds total)