Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/11_2022/7jv2_22491.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/11_2022/7jv2_22491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/11_2022/7jv2_22491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/11_2022/7jv2_22491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/11_2022/7jv2_22491.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv2_22491/11_2022/7jv2_22491.pdb" } resolution = 3.5 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= 0.023 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2151 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain breaks: 1 Time building chain proxies: 2.05, per 1000 atoms: 0.95 Number of scatterers: 2151 At special positions: 0 Unit cell: (68.25, 55.65, 66.15, 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 8 16.00 O 419 8.00 N 363 7.00 C 1361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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: 0.87 Conformation dependent library (CDL) restraints added in 342.6 milliseconds 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 494 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 5.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.839A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.513A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 90 hydrogen bonds defined for protein. 195 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: 0.62 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 459 1.32 - 1.45: 593 1.45 - 1.57: 1134 1.57 - 1.69: 8 1.69 - 1.82: 10 Bond restraints: 2204 Sorted by residual: bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.623 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 1.530 1.610 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CB LEU L 110 " pdb=" CG LEU L 110 " ideal model delta sigma weight residual 1.530 1.597 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ILE H 70 " pdb=" CG1 ILE H 70 " ideal model delta sigma weight residual 1.530 1.468 0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" CG GLN L 1 " pdb=" CD GLN L 1 " ideal model delta sigma weight residual 1.516 1.587 -0.071 2.50e-02 1.60e+03 8.01e+00 ... (remaining 2199 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.41: 86 107.41 - 114.01: 1118 114.01 - 120.62: 963 120.62 - 127.22: 805 127.22 - 133.82: 19 Bond angle restraints: 2991 Sorted by residual: angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.82 126.78 -6.96 9.80e-01 1.04e+00 5.04e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 125.42 -5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" C GLU L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.32 125.73 -6.41 1.14e+00 7.69e-01 3.16e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.76 125.21 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C ARG L 81 " pdb=" N PRO L 82 " pdb=" CA PRO L 82 " ideal model delta sigma weight residual 119.47 125.67 -6.20 1.16e+00 7.43e-01 2.86e+01 ... (remaining 2986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1219 17.29 - 34.57: 35 34.57 - 51.85: 10 51.85 - 69.14: 3 69.14 - 86.42: 5 Dihedral angle restraints: 1272 sinusoidal: 479 harmonic: 793 Sorted by residual: dihedral pdb=" CB GLU H 46 " pdb=" CG GLU H 46 " pdb=" CD GLU H 46 " pdb=" OE1 GLU H 46 " ideal model delta sinusoidal sigma weight residual 0.00 -86.42 86.42 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" N TYR H 59 " pdb=" CA TYR H 59 " pdb=" CB TYR H 59 " pdb=" CG TYR H 59 " ideal model delta sinusoidal sigma weight residual -180.00 -123.33 -56.67 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sinusoidal sigma weight residual 0.00 -82.50 82.50 1 3.00e+01 1.11e-03 9.27e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 216 0.069 - 0.139: 85 0.139 - 0.208: 11 0.208 - 0.277: 2 0.277 - 0.347: 2 Chirality restraints: 316 Sorted by residual: chirality pdb=" CG LEU L 110 " pdb=" CB LEU L 110 " pdb=" CD1 LEU L 110 " pdb=" CD2 LEU L 110 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 313 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 32 " -0.042 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR H 32 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR H 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 32 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 32 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 32 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR H 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 32 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 105 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.94e+00 pdb=" CG TYR H 105 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 105 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 105 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 105 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR H 105 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR H 105 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 105 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " 0.030 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " 0.015 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1312 3.05 - 3.51: 1905 3.51 - 3.97: 3466 3.97 - 4.44: 3915 4.44 - 4.90: 6436 Nonbonded interactions: 17034 Sorted by model distance: nonbonded pdb=" N HIS L 33 " pdb=" N TYR L 34 " model vdw 2.587 2.560 nonbonded pdb=" N LYS H 76 " pdb=" N ASN H 77 " model vdw 2.587 2.560 nonbonded pdb=" N SER H 71 " pdb=" O SER H 71 " model vdw 2.589 2.496 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.594 2.520 nonbonded pdb=" O TYR L 34 " pdb=" CB TYR L 34 " model vdw 2.596 2.752 ... (remaining 17029 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 1361 2.51 5 N 363 2.21 5 O 419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.390 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: 12.170 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.190 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.015 0.093 2204 Z= 0.946 Angle : 1.386 6.959 2991 Z= 0.934 Chirality : 0.075 0.347 316 Planarity : 0.006 0.022 385 Dihedral : 11.432 86.421 769 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 1.32 % 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: 0.82 (0.50), residues: 274 helix: None (None), residues: 0 sheet: 0.23 (0.50), residues: 102 loop : 0.93 (0.47), residues: 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.243 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 65 average time/residue: 0.1495 time to fit residues: 11.2466 Evaluate side-chains 45 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 21 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 0.4980 overall best weight: 0.1156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN L 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 2204 Z= 0.166 Angle : 0.599 7.459 2991 Z= 0.318 Chirality : 0.042 0.150 316 Planarity : 0.003 0.022 385 Dihedral : 4.486 15.142 310 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.20 % 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: 0.53 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.24 (0.46), residues: 112 loop : 0.60 (0.47), residues: 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.245 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.1324 time to fit residues: 8.1874 Evaluate side-chains 49 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0265 time to fit residues: 0.4664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 18 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 2204 Z= 0.372 Angle : 0.715 7.656 2991 Z= 0.380 Chirality : 0.046 0.150 316 Planarity : 0.004 0.026 385 Dihedral : 5.148 16.511 310 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 2.64 % 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: 0.16 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.40 (0.48), residues: 110 loop : -0.02 (0.45), residues: 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.248 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1164 time to fit residues: 7.0922 Evaluate side-chains 47 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.240 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0258 time to fit residues: 0.5209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.0370 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 2204 Z= 0.339 Angle : 0.691 7.302 2991 Z= 0.364 Chirality : 0.044 0.142 316 Planarity : 0.004 0.024 385 Dihedral : 5.240 17.851 310 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 2.64 % 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: -0.30 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.04 (0.46), residues: 115 loop : -0.29 (0.47), residues: 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.246 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1209 time to fit residues: 7.3675 Evaluate side-chains 52 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0316 time to fit residues: 0.5966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 15 optimal weight: 0.0010 overall best weight: 0.3386 ------------------------------------------------------------------------------- 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: 0.7708 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 2204 Z= 0.289 Angle : 0.655 7.132 2991 Z= 0.343 Chirality : 0.043 0.134 316 Planarity : 0.004 0.029 385 Dihedral : 5.077 18.590 310 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 3.52 % 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: -0.60 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.21 (0.46), residues: 112 loop : -0.47 (0.46), residues: 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.249 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1080 time to fit residues: 6.8358 Evaluate side-chains 51 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0251 time to fit residues: 0.6352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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: 0.7686 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 2204 Z= 0.246 Angle : 0.620 6.798 2991 Z= 0.323 Chirality : 0.042 0.132 316 Planarity : 0.004 0.033 385 Dihedral : 4.853 18.415 310 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 2.64 % 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: -0.75 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.29 (0.48), residues: 107 loop : -0.59 (0.46), residues: 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.241 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1147 time to fit residues: 7.2744 Evaluate side-chains 51 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0861 time to fit residues: 0.8616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 2204 Z= 0.399 Angle : 0.720 7.004 2991 Z= 0.378 Chirality : 0.045 0.148 316 Planarity : 0.004 0.033 385 Dihedral : 5.287 19.071 310 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 1.76 % 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: -1.10 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -0.57 (0.47), residues: 107 loop : -0.80 (0.46), residues: 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.297 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1032 time to fit residues: 6.2591 Evaluate side-chains 47 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0253 time to fit residues: 0.4693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.0570 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.0060 chunk 17 optimal weight: 0.0050 overall best weight: 0.0386 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 2204 Z= 0.132 Angle : 0.571 7.932 2991 Z= 0.292 Chirality : 0.040 0.120 316 Planarity : 0.004 0.038 385 Dihedral : 4.451 17.504 310 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.76 % 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 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -0.40 (0.47), residues: 110 loop : -0.40 (0.48), residues: 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.273 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1110 time to fit residues: 6.4701 Evaluate side-chains 45 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0321 time to fit residues: 0.4851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 2204 Z= 0.333 Angle : 0.704 7.863 2991 Z= 0.363 Chirality : 0.044 0.134 316 Planarity : 0.004 0.036 385 Dihedral : 4.995 18.260 310 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % 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: -0.94 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -0.53 (0.49), residues: 105 loop : -0.63 (0.46), residues: 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1140 time to fit residues: 6.3634 Evaluate side-chains 43 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 2204 Z= 0.286 Angle : 0.686 7.929 2991 Z= 0.353 Chirality : 0.043 0.132 316 Planarity : 0.004 0.035 385 Dihedral : 5.017 20.169 310 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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: -1.12 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.71 (0.48), residues: 105 loop : -0.72 (0.46), residues: 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1048 time to fit residues: 5.7591 Evaluate side-chains 43 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.0050 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137747 restraints weight = 3148.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140139 restraints weight = 1847.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141666 restraints weight = 1227.592| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 2204 Z= 0.295 Angle : 0.698 7.911 2991 Z= 0.353 Chirality : 0.043 0.132 316 Planarity : 0.004 0.035 385 Dihedral : 5.010 19.971 310 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.44 % 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: -1.20 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.76 (0.49), residues: 105 loop : -0.77 (0.45), residues: 169 =============================================================================== Job complete usr+sys time: 1168.02 seconds wall clock time: 21 minutes 32.46 seconds (1292.46 seconds total)