Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 23:34:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/07_2023/8exa_28656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/07_2023/8exa_28656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/07_2023/8exa_28656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/07_2023/8exa_28656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/07_2023/8exa_28656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exa_28656/07_2023/8exa_28656.pdb" } resolution = 3.14 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 139 5.49 5 S 2 5.16 5 C 2984 2.51 5 N 1029 2.21 5 O 1385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 5539 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2610 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2163 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 49, 'rna3p_pyr': 42} Link IDs: {'rna2p': 10, 'rna3p': 90} Chain breaks: 2 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 252 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {' DC:plan2': 1, ' DC:plan': 1, ' DT:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Time building chain proxies: 3.88, per 1000 atoms: 0.70 Number of scatterers: 5539 At special positions: 0 Unit cell: (81.4, 86.9, 97.9, 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 2 16.00 P 139 15.00 O 1385 8.00 N 1029 7.00 C 2984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 564.0 milliseconds 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 2 sheets defined 53.7% alpha, 15.2% beta 56 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 14 through 46 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 75 through 96 removed outlier: 3.714A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.628A pdb=" N LEU A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 121 removed outlier: 7.383A pdb=" N ILE A 154 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU A 174 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 156 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209 removed outlier: 4.215A pdb=" N VAL A 200 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A 278 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 192 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL A 321 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A 277 " --> pdb=" O VAL A 321 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 923 1.33 - 1.45: 2154 1.45 - 1.57: 2579 1.57 - 1.69: 273 1.69 - 1.80: 3 Bond restraints: 5932 Sorted by residual: bond pdb=" N GLN A 80 " pdb=" CA GLN A 80 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.23e-02 6.61e+03 3.44e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.46e-01 bond pdb=" C3' DC C 3 " pdb=" O3' DC C 3 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.34e-01 bond pdb=" C4' DT C 0 " pdb=" O4' DT C 0 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 6.97e-01 bond pdb=" CA GLN A 80 " pdb=" C GLN A 80 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.29e-02 6.01e+03 6.52e-01 ... (remaining 5927 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.12: 903 107.12 - 113.83: 3490 113.83 - 120.55: 2281 120.55 - 127.26: 1693 127.26 - 133.97: 306 Bond angle restraints: 8673 Sorted by residual: angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 118.72 -4.82 1.80e+00 3.09e-01 7.18e+00 angle pdb=" C2' G B 3 " pdb=" C1' G B 3 " pdb=" N9 G B 3 " ideal model delta sigma weight residual 112.00 115.28 -3.28 1.50e+00 4.44e-01 4.79e+00 angle pdb=" N ILE A 275 " pdb=" CA ILE A 275 " pdb=" C ILE A 275 " ideal model delta sigma weight residual 106.53 109.29 -2.76 1.41e+00 5.03e-01 3.83e+00 angle pdb=" C2' U B 9 " pdb=" C1' U B 9 " pdb=" N1 U B 9 " ideal model delta sigma weight residual 114.00 111.36 2.64 1.50e+00 4.44e-01 3.10e+00 angle pdb=" C4' DG C -5 " pdb=" O4' DG C -5 " pdb=" C1' DG C -5 " ideal model delta sigma weight residual 109.70 107.08 2.62 1.50e+00 4.44e-01 3.05e+00 ... (remaining 8668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 2908 28.56 - 57.13: 234 57.13 - 85.69: 31 85.69 - 114.25: 1 114.25 - 142.82: 1 Dihedral angle restraints: 3175 sinusoidal: 2186 harmonic: 989 Sorted by residual: dihedral pdb=" C4' DC C 3 " pdb=" C3' DC C 3 " pdb=" O3' DC C 3 " pdb=" P DA C 4 " ideal model delta sinusoidal sigma weight residual 220.00 77.18 142.82 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -119.23 -40.77 1 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA LEU A 136 " pdb=" C LEU A 136 " pdb=" N PRO A 137 " pdb=" CA PRO A 137 " ideal model delta harmonic sigma weight residual -180.00 -164.05 -15.95 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 769 0.030 - 0.060: 213 0.060 - 0.090: 47 0.090 - 0.119: 26 0.119 - 0.149: 7 Chirality restraints: 1062 Sorted by residual: chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" C1' A B 2 " pdb=" O4' A B 2 " pdb=" C2' A B 2 " pdb=" N9 A B 2 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA PRO A 137 " pdb=" N PRO A 137 " pdb=" C PRO A 137 " pdb=" CB PRO A 137 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1059 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.031 2.00e-02 2.50e+03 1.28e-02 4.95e+00 pdb=" N9 G B 3 " 0.028 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 3 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 9 " 0.026 2.00e-02 2.50e+03 1.39e-02 4.35e+00 pdb=" N1 U B 9 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 9 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 9 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 2 " -0.023 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A B 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A B 2 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 2 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 2 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 2 " 0.003 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 899 2.76 - 3.29: 5072 3.29 - 3.83: 11101 3.83 - 4.36: 12729 4.36 - 4.90: 18341 Nonbonded interactions: 48142 Sorted by model distance: nonbonded pdb=" OG SER A 117 " pdb=" OP1 U B 4 " model vdw 2.223 2.440 nonbonded pdb=" O2 C B-107 " pdb=" N2 G B -6 " model vdw 2.251 2.520 nonbonded pdb=" NH1 ARG A 39 " pdb=" OE1 GLU A 87 " model vdw 2.275 2.520 nonbonded pdb=" N2 G B-114 " pdb=" O4 U B -89 " model vdw 2.301 2.520 nonbonded pdb=" NH1 ARG A 110 " pdb=" OP1 C B 5 " model vdw 2.319 2.520 ... (remaining 48137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.240 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 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 : 0.004 0.029 5932 Z= 0.219 Angle : 0.538 4.927 8673 Z= 0.286 Chirality : 0.033 0.149 1062 Planarity : 0.003 0.023 596 Dihedral : 17.450 142.816 2539 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.40 % 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: 0.27 (0.47), residues: 337 helix: 1.86 (0.40), residues: 175 sheet: -1.83 (0.63), residues: 65 loop : -1.41 (0.60), residues: 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.363 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2042 time to fit residues: 12.1559 Evaluate side-chains 38 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0536 time to fit residues: 0.6485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 227 GLN A 250 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5932 Z= 0.200 Angle : 0.513 5.436 8673 Z= 0.273 Chirality : 0.032 0.126 1062 Planarity : 0.003 0.026 596 Dihedral : 18.099 142.566 1956 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 3.24 % 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: 0.80 (0.48), residues: 337 helix: 2.43 (0.39), residues: 168 sheet: -1.83 (0.65), residues: 66 loop : -0.99 (0.61), residues: 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.421 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 49 average time/residue: 0.2253 time to fit residues: 13.9133 Evaluate side-chains 41 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0637 time to fit residues: 0.7936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 5932 Z= 0.420 Angle : 0.704 7.057 8673 Z= 0.367 Chirality : 0.041 0.160 1062 Planarity : 0.005 0.033 596 Dihedral : 18.415 143.606 1956 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 3.64 % 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: -0.26 (0.47), residues: 337 helix: 1.33 (0.38), residues: 176 sheet: -1.87 (0.67), residues: 67 loop : -1.62 (0.60), residues: 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.424 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.2345 time to fit residues: 14.1166 Evaluate side-chains 44 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0513 time to fit residues: 1.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5932 Z= 0.143 Angle : 0.479 4.473 8673 Z= 0.258 Chirality : 0.031 0.153 1062 Planarity : 0.003 0.022 596 Dihedral : 17.961 142.717 1956 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.48), residues: 337 helix: 2.53 (0.39), residues: 168 sheet: -1.72 (0.66), residues: 66 loop : -1.23 (0.59), residues: 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.436 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 39 average time/residue: 0.2336 time to fit residues: 11.5950 Evaluate side-chains 33 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0571 time to fit residues: 0.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 5932 Z= 0.246 Angle : 0.542 6.126 8673 Z= 0.288 Chirality : 0.033 0.128 1062 Planarity : 0.004 0.027 596 Dihedral : 18.071 143.207 1956 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.48), residues: 337 helix: 1.96 (0.39), residues: 177 sheet: -1.81 (0.66), residues: 67 loop : -1.45 (0.62), residues: 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.436 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.3008 time to fit residues: 14.8888 Evaluate side-chains 34 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0547 time to fit residues: 0.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5932 Z= 0.220 Angle : 0.540 10.293 8673 Z= 0.283 Chirality : 0.033 0.127 1062 Planarity : 0.004 0.035 596 Dihedral : 18.033 142.943 1956 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.47), residues: 337 helix: 1.93 (0.38), residues: 177 sheet: -1.76 (0.66), residues: 66 loop : -1.46 (0.61), residues: 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.423 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.2740 time to fit residues: 13.4679 Evaluate side-chains 39 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0558 time to fit residues: 0.7957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.0770 chunk 38 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5932 Z= 0.132 Angle : 0.472 9.836 8673 Z= 0.250 Chirality : 0.029 0.126 1062 Planarity : 0.003 0.032 596 Dihedral : 17.856 142.147 1956 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.81 % 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: 0.97 (0.48), residues: 337 helix: 2.58 (0.38), residues: 170 sheet: -1.56 (0.66), residues: 66 loop : -1.18 (0.61), residues: 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.387 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.2673 time to fit residues: 11.7976 Evaluate side-chains 35 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0796 time to fit residues: 0.5773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 5932 Z= 0.344 Angle : 0.638 8.568 8673 Z= 0.333 Chirality : 0.037 0.140 1062 Planarity : 0.005 0.036 596 Dihedral : 18.200 143.345 1956 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.40 % 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: 0.08 (0.47), residues: 337 helix: 1.65 (0.39), residues: 177 sheet: -1.81 (0.66), residues: 67 loop : -1.51 (0.63), residues: 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.481 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.3098 time to fit residues: 15.2793 Evaluate side-chains 38 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0582 time to fit residues: 0.6228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 5932 Z= 0.268 Angle : 0.592 8.547 8673 Z= 0.307 Chirality : 0.035 0.134 1062 Planarity : 0.004 0.035 596 Dihedral : 18.119 143.871 1956 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.21 % 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: 0.05 (0.47), residues: 337 helix: 1.64 (0.39), residues: 177 sheet: -1.86 (0.66), residues: 67 loop : -1.56 (0.61), residues: 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.415 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 0.3012 time to fit residues: 14.8372 Evaluate side-chains 41 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0542 time to fit residues: 0.5719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5932 Z= 0.191 Angle : 0.541 8.758 8673 Z= 0.282 Chirality : 0.032 0.139 1062 Planarity : 0.004 0.031 596 Dihedral : 18.017 143.469 1956 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: 0.22 (0.47), residues: 337 helix: 1.81 (0.39), residues: 177 sheet: -1.80 (0.66), residues: 66 loop : -1.54 (0.61), residues: 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.3132 time to fit residues: 13.9035 Evaluate side-chains 34 residues out of total 289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.198879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159407 restraints weight = 7308.903| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.64 r_work: 0.3844 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5932 Z= 0.152 Angle : 0.505 8.426 8673 Z= 0.263 Chirality : 0.030 0.124 1062 Planarity : 0.004 0.037 596 Dihedral : 17.886 142.515 1956 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.40 % 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: 0.46 (0.47), residues: 337 helix: 2.00 (0.38), residues: 177 sheet: -1.58 (0.67), residues: 66 loop : -1.53 (0.60), residues: 94 =============================================================================== Job complete usr+sys time: 1193.15 seconds wall clock time: 22 minutes 30.82 seconds (1350.82 seconds total)