Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:47:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/04_2023/8ctk_26993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/04_2023/8ctk_26993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/04_2023/8ctk_26993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/04_2023/8ctk_26993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/04_2023/8ctk_26993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctk_26993/04_2023/8ctk_26993.pdb" } resolution = 3.52 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= 0.018 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2020 2.51 5 N 520 2.21 5 O 488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3042 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Time building chain proxies: 2.08, per 1000 atoms: 0.68 Number of scatterers: 3042 At special positions: 0 Unit cell: (74.881, 54.525, 80.697, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 488 8.00 N 520 7.00 C 2020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 429.6 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 48.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.836A pdb=" N ASN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 56 through 71 removed outlier: 4.123A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 107 removed outlier: 3.853A pdb=" N GLY A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.733A pdb=" N ASN A 113 " --> pdb=" O TRP A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 38 removed outlier: 3.622A pdb=" N LEU B 35 " --> pdb=" O TRP B 31 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 71 removed outlier: 4.123A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 107 removed outlier: 3.852A pdb=" N GLY B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.732A pdb=" N ASN B 113 " --> pdb=" O TRP B 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 132 removed outlier: 7.079A pdb=" N GLU A 167 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 176 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR A 178 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA A 195 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER A 184 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 193 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.079A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 176 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 178 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA B 195 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER B 184 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 193 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 924 1.34 - 1.46: 773 1.46 - 1.58: 1409 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3126 Sorted by residual: bond pdb=" CB ASP B 190 " pdb=" CG ASP B 190 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" C TRP A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.29e-01 bond pdb=" C TRP B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.67e-01 bond pdb=" CB ASP A 160 " pdb=" CG ASP A 160 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.36e-01 ... (remaining 3121 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.34: 66 106.34 - 113.25: 1679 113.25 - 120.15: 1102 120.15 - 127.05: 1361 127.05 - 133.95: 46 Bond angle restraints: 4254 Sorted by residual: angle pdb=" N ILE B 73 " pdb=" CA ILE B 73 " pdb=" C ILE B 73 " ideal model delta sigma weight residual 111.62 107.80 3.82 7.90e-01 1.60e+00 2.34e+01 angle pdb=" N ILE A 73 " pdb=" CA ILE A 73 " pdb=" C ILE A 73 " ideal model delta sigma weight residual 111.62 107.82 3.80 7.90e-01 1.60e+00 2.31e+01 angle pdb=" CA MET B 91 " pdb=" CB MET B 91 " pdb=" CG MET B 91 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 7.00e+00 angle pdb=" CA MET A 91 " pdb=" CB MET A 91 " pdb=" CG MET A 91 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.90e+00 angle pdb=" CA LEU A 56 " pdb=" CB LEU A 56 " pdb=" CG LEU A 56 " ideal model delta sigma weight residual 116.30 124.34 -8.04 3.50e+00 8.16e-02 5.28e+00 ... (remaining 4249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 1512 13.01 - 26.02: 170 26.02 - 39.03: 78 39.03 - 52.03: 22 52.03 - 65.04: 6 Dihedral angle restraints: 1788 sinusoidal: 696 harmonic: 1092 Sorted by residual: dihedral pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " pdb=" CZ ARG A 198 " ideal model delta sinusoidal sigma weight residual 180.00 135.44 44.56 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 198 " pdb=" CD ARG B 198 " pdb=" NE ARG B 198 " pdb=" CZ ARG B 198 " ideal model delta sinusoidal sigma weight residual 180.00 135.49 44.51 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" N MET A 84 " pdb=" CA MET A 84 " pdb=" CB MET A 84 " pdb=" CG MET A 84 " ideal model delta sinusoidal sigma weight residual -60.00 -113.00 53.00 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 1785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 354 0.045 - 0.090: 99 0.090 - 0.134: 30 0.134 - 0.179: 1 0.179 - 0.224: 2 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA ILE A 118 " pdb=" N ILE A 118 " pdb=" C ILE A 118 " pdb=" CB ILE A 118 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 118 " pdb=" N ILE B 118 " pdb=" C ILE B 118 " pdb=" CB ILE B 118 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A 143 " pdb=" N VAL A 143 " pdb=" C VAL A 143 " pdb=" CB VAL A 143 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 483 not shown) Planarity restraints: 512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 31 " 0.025 2.00e-02 2.50e+03 1.49e-02 5.55e+00 pdb=" CG TRP A 31 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 31 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 31 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 31 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 31 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 31 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 31 " -0.025 2.00e-02 2.50e+03 1.48e-02 5.44e+00 pdb=" CG TRP B 31 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 31 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 31 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 31 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 31 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 31 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 31 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 193 " -0.012 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 193 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 193 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 193 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 193 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 193 " 0.005 2.00e-02 2.50e+03 ... (remaining 509 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1035 2.86 - 3.37: 2693 3.37 - 3.88: 4899 3.88 - 4.39: 5175 4.39 - 4.90: 8964 Nonbonded interactions: 22766 Sorted by model distance: nonbonded pdb=" O PRO A 132 " pdb=" NE2 HIS A 154 " model vdw 2.347 2.520 nonbonded pdb=" O PRO B 132 " pdb=" NE2 HIS B 154 " model vdw 2.348 2.520 nonbonded pdb=" O VAL A 187 " pdb=" OG SER A 191 " model vdw 2.395 2.440 nonbonded pdb=" O VAL B 187 " pdb=" OG SER B 191 " model vdw 2.395 2.440 nonbonded pdb=" N GLU B 137 " pdb=" OE1 GLU B 137 " model vdw 2.407 2.520 ... (remaining 22761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.990 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: 0.000 Extract box with map and model: 5.090 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.390 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 : 0.003 0.035 3126 Z= 0.214 Angle : 0.691 8.040 4254 Z= 0.364 Chirality : 0.047 0.224 486 Planarity : 0.005 0.043 512 Dihedral : 14.365 65.043 1088 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.43), residues: 372 helix: 0.55 (0.41), residues: 164 sheet: -0.63 (0.60), residues: 78 loop : -2.38 (0.48), residues: 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1135 time to fit residues: 7.8476 Evaluate side-chains 49 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 3126 Z= 0.206 Angle : 0.529 6.653 4254 Z= 0.273 Chirality : 0.042 0.181 486 Planarity : 0.004 0.036 512 Dihedral : 3.599 11.674 420 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.90 % 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: -0.84 (0.43), residues: 372 helix: 0.92 (0.41), residues: 166 sheet: -0.89 (0.59), residues: 78 loop : -2.30 (0.49), residues: 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.1072 time to fit residues: 7.6623 Evaluate side-chains 56 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0317 time to fit residues: 0.7034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.6961 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3126 Z= 0.184 Angle : 0.513 5.631 4254 Z= 0.262 Chirality : 0.042 0.182 486 Planarity : 0.004 0.034 512 Dihedral : 3.554 11.564 420 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.90 % 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: -0.74 (0.43), residues: 372 helix: 1.09 (0.40), residues: 166 sheet: -0.97 (0.59), residues: 78 loop : -2.29 (0.49), residues: 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.292 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.0955 time to fit residues: 7.5629 Evaluate side-chains 57 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0403 time to fit residues: 0.7561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7025 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 3126 Z= 0.231 Angle : 0.537 5.255 4254 Z= 0.274 Chirality : 0.043 0.182 486 Planarity : 0.004 0.030 512 Dihedral : 3.588 12.387 420 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 3.16 % 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: -0.75 (0.43), residues: 372 helix: 1.19 (0.40), residues: 164 sheet: -1.13 (0.57), residues: 78 loop : -2.30 (0.47), residues: 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.392 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.0915 time to fit residues: 7.4872 Evaluate side-chains 57 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0334 time to fit residues: 0.8327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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: 0.7016 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 3126 Z= 0.203 Angle : 0.516 5.723 4254 Z= 0.264 Chirality : 0.043 0.180 486 Planarity : 0.004 0.027 512 Dihedral : 3.533 11.716 420 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.58 % 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: -0.62 (0.43), residues: 372 helix: 1.27 (0.40), residues: 166 sheet: -1.11 (0.58), residues: 78 loop : -2.20 (0.48), residues: 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.0888 time to fit residues: 6.7946 Evaluate side-chains 56 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0381 time to fit residues: 0.7270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7074 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 3126 Z= 0.258 Angle : 0.556 7.230 4254 Z= 0.281 Chirality : 0.043 0.181 486 Planarity : 0.004 0.026 512 Dihedral : 3.641 11.235 420 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 1.90 % 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: -0.67 (0.43), residues: 372 helix: 1.37 (0.40), residues: 164 sheet: -1.30 (0.56), residues: 78 loop : -2.27 (0.47), residues: 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.0868 time to fit residues: 6.9155 Evaluate side-chains 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0303 time to fit residues: 0.5448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7036 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 3126 Z= 0.204 Angle : 0.533 6.719 4254 Z= 0.269 Chirality : 0.043 0.179 486 Planarity : 0.004 0.025 512 Dihedral : 3.531 11.403 420 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.63 % 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: -0.55 (0.43), residues: 372 helix: 1.25 (0.40), residues: 170 sheet: -1.12 (0.57), residues: 78 loop : -2.12 (0.49), residues: 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.336 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.0995 time to fit residues: 6.9940 Evaluate side-chains 53 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0541 time to fit residues: 0.5618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.7048 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 3126 Z= 0.216 Angle : 0.535 6.438 4254 Z= 0.269 Chirality : 0.043 0.177 486 Planarity : 0.004 0.025 512 Dihedral : 3.537 11.280 420 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.27 % 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: -0.55 (0.43), residues: 372 helix: 1.36 (0.40), residues: 168 sheet: -1.19 (0.58), residues: 78 loop : -2.18 (0.47), residues: 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.0854 time to fit residues: 6.6411 Evaluate side-chains 57 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0376 time to fit residues: 0.6190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3126 Z= 0.207 Angle : 0.534 6.337 4254 Z= 0.271 Chirality : 0.043 0.178 486 Planarity : 0.004 0.027 512 Dihedral : 3.519 11.067 420 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.44), residues: 372 helix: 1.41 (0.41), residues: 168 sheet: -1.08 (0.59), residues: 78 loop : -2.10 (0.48), residues: 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.305 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0907 time to fit residues: 6.5410 Evaluate side-chains 52 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.0670 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3126 Z= 0.174 Angle : 0.520 6.182 4254 Z= 0.265 Chirality : 0.042 0.172 486 Planarity : 0.004 0.029 512 Dihedral : 3.399 11.251 420 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.32 % 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: 0.03 (0.44), residues: 372 helix: 1.99 (0.41), residues: 156 sheet: -0.93 (0.60), residues: 78 loop : -1.75 (0.50), residues: 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.362 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.0959 time to fit residues: 6.8626 Evaluate side-chains 49 residues out of total 316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 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 = 0.4507 r_free = 0.4507 target = 0.215495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178404 restraints weight = 3624.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.182223 restraints weight = 2455.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.184913 restraints weight = 1903.332| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 3126 Z= 0.241 Angle : 0.559 6.067 4254 Z= 0.285 Chirality : 0.044 0.209 486 Planarity : 0.004 0.026 512 Dihedral : 3.520 11.059 420 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.63 % 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: -0.33 (0.44), residues: 372 helix: 1.50 (0.41), residues: 168 sheet: -1.06 (0.60), residues: 78 loop : -2.01 (0.48), residues: 126 =============================================================================== Job complete usr+sys time: 1069.25 seconds wall clock time: 19 minutes 39.79 seconds (1179.79 seconds total)