Starting phenix.real_space_refine on Mon Sep 23 11:42:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/09_2024/7m64_23688.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/09_2024/7m64_23688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/09_2024/7m64_23688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/09_2024/7m64_23688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/09_2024/7m64_23688.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/09_2024/7m64_23688.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1140 2.51 5 N 330 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1850 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 0.79, per 1000 atoms: 0.43 Number of scatterers: 1850 At special positions: 0 Unit cell: (48.53, 66.465, 44.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 380 8.00 N 330 7.00 C 1140 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 - 3.00 Amino acid : True - 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 206.6 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.145A pdb=" N PHE D 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE A 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE E 15 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE I 15 " --> pdb=" O ASN E 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 27 through 28 removed outlier: 6.871A pdb=" N LEU A 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 27 " --> pdb=" O SER I 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.570A pdb=" N PHE G 15 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 15 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE F 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.871A pdb=" N LEU C 27 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 27 " --> pdb=" O SER C 28 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.33 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 300 1.29 - 1.36: 313 1.36 - 1.43: 267 1.43 - 1.50: 297 1.50 - 1.56: 693 Bond restraints: 1870 Sorted by residual: bond pdb=" N ALA B 13 " pdb=" CA ALA B 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N ALA E 13 " pdb=" CA ALA E 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.32e+00 bond pdb=" C ALA C 13 " pdb=" N ASN C 14 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.25e-02 6.40e+03 4.29e+00 bond pdb=" N ALA F 13 " pdb=" CA ALA F 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 bond pdb=" N ALA H 13 " pdb=" CA ALA H 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 ... (remaining 1865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 1993 1.17 - 2.34: 385 2.34 - 3.51: 114 3.51 - 4.68: 38 4.68 - 5.85: 10 Bond angle restraints: 2540 Sorted by residual: angle pdb=" C ALA H 13 " pdb=" CA ALA H 13 " pdb=" CB ALA H 13 " ideal model delta sigma weight residual 110.50 116.35 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta sigma weight residual 110.50 116.34 -5.84 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA B 13 " pdb=" CA ALA B 13 " pdb=" CB ALA B 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA F 13 " pdb=" CA ALA F 13 " pdb=" CB ALA F 13 " ideal model delta sigma weight residual 110.50 116.32 -5.82 1.50e+00 4.44e-01 1.51e+01 ... (remaining 2535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.60: 760 5.60 - 11.20: 140 11.20 - 16.80: 59 16.80 - 22.40: 61 22.40 - 27.99: 20 Dihedral angle restraints: 1040 sinusoidal: 330 harmonic: 710 Sorted by residual: dihedral pdb=" C ALA J 13 " pdb=" N ALA J 13 " pdb=" CA ALA J 13 " pdb=" CB ALA J 13 " ideal model delta harmonic sigma weight residual -122.60 -132.53 9.93 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" C ALA C 13 " pdb=" N ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta harmonic sigma weight residual -122.60 -132.51 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C ALA E 13 " pdb=" N ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta harmonic sigma weight residual -122.60 -132.49 9.89 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 1037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 224 0.045 - 0.090: 36 0.090 - 0.135: 11 0.135 - 0.179: 9 0.179 - 0.224: 20 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA ALA J 13 " pdb=" N ALA J 13 " pdb=" C ALA J 13 " pdb=" CB ALA J 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA C 13 " pdb=" N ALA C 13 " pdb=" C ALA C 13 " pdb=" CB ALA C 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ALA G 13 " pdb=" N ALA G 13 " pdb=" C ALA G 13 " pdb=" CB ALA G 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 297 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 13 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA F 13 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA F 13 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN F 14 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 13 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA C 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA C 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 13 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA H 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA H 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN H 14 " -0.008 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 998 2.94 - 3.43: 2256 3.43 - 3.92: 2945 3.92 - 4.41: 3321 4.41 - 4.90: 6387 Nonbonded interactions: 15907 Sorted by model distance: nonbonded pdb=" OG SER I 19 " pdb=" OD1 ASN I 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER J 19 " pdb=" OD1 ASN J 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER G 19 " pdb=" OD1 ASN G 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER A 19 " pdb=" OD1 ASN A 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER D 19 " pdb=" OD1 ASN D 22 " model vdw 2.451 3.040 ... (remaining 15902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.120 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.008 0.040 1870 Z= 0.512 Angle : 1.155 5.847 2540 Z= 0.676 Chirality : 0.068 0.224 300 Planarity : 0.004 0.013 330 Dihedral : 10.068 27.994 580 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.40), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 18 PHE 0.009 0.002 PHE F 23 TYR 0.003 0.001 TYR F 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0695 time to fit residues: 2.8596 Evaluate side-chains 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.7512 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1870 Z= 0.233 Angle : 0.840 7.217 2540 Z= 0.422 Chirality : 0.045 0.123 300 Planarity : 0.003 0.009 330 Dihedral : 4.369 13.327 250 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 14.29 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.008 0.002 PHE H 23 TYR 0.005 0.001 TYR J 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.236 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.0692 time to fit residues: 2.5099 Evaluate side-chains 26 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.0040 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 40.0000 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 overall best weight: 4.0000 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 1870 Z= 0.173 Angle : 0.750 7.153 2540 Z= 0.374 Chirality : 0.046 0.159 300 Planarity : 0.002 0.008 330 Dihedral : 3.925 10.997 250 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.48 % Allowed : 14.76 % Favored : 84.76 % 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: -4.16 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 18 PHE 0.008 0.001 PHE C 15 TYR 0.003 0.001 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.224 Fit side-chains REVERT: B 27 LEU cc_start: 0.8786 (mp) cc_final: 0.8127 (tt) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0653 time to fit residues: 2.4886 Evaluate side-chains 22 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1870 Z= 0.338 Angle : 0.860 5.857 2540 Z= 0.451 Chirality : 0.047 0.137 300 Planarity : 0.003 0.010 330 Dihedral : 4.775 12.822 250 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.86 % Allowed : 14.76 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 18 PHE 0.013 0.003 PHE E 15 TYR 0.009 0.002 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.173 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 19 average time/residue: 0.0750 time to fit residues: 2.0215 Evaluate side-chains 19 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1870 Z= 0.286 Angle : 0.820 5.942 2540 Z= 0.417 Chirality : 0.045 0.137 300 Planarity : 0.003 0.011 330 Dihedral : 4.673 13.173 250 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 19.05 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.35), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.011 0.002 PHE C 15 TYR 0.006 0.001 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.234 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.0682 time to fit residues: 1.7021 Evaluate side-chains 15 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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: 0.7522 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1870 Z= 0.188 Angle : 0.747 5.985 2540 Z= 0.373 Chirality : 0.044 0.135 300 Planarity : 0.002 0.011 330 Dihedral : 4.388 13.088 250 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 19.52 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.009 0.002 PHE E 15 TYR 0.003 0.001 TYR J 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0597 time to fit residues: 1.5834 Evaluate side-chains 13 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 0.0370 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 overall best weight: 6.2066 ------------------------------------------------------------------------------- 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: 0.7550 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1870 Z= 0.214 Angle : 0.776 8.450 2540 Z= 0.389 Chirality : 0.044 0.135 300 Planarity : 0.002 0.011 330 Dihedral : 4.450 12.943 250 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 18.57 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.011 0.002 PHE C 15 TYR 0.004 0.001 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.218 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.0644 time to fit residues: 1.6718 Evaluate side-chains 15 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 16 optimal weight: 40.0000 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7527 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1870 Z= 0.206 Angle : 0.776 8.382 2540 Z= 0.386 Chirality : 0.044 0.135 300 Planarity : 0.002 0.012 330 Dihedral : 4.443 13.383 250 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 19.05 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 18 PHE 0.009 0.002 PHE E 15 TYR 0.004 0.001 TYR G 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.226 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0642 time to fit residues: 1.5841 Evaluate side-chains 16 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 40.0000 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 1870 Z= 0.382 Angle : 0.889 8.700 2540 Z= 0.459 Chirality : 0.046 0.140 300 Planarity : 0.003 0.013 330 Dihedral : 5.056 13.811 250 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.43 % Allowed : 18.10 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 18 PHE 0.012 0.003 PHE C 15 TYR 0.010 0.002 TYR E 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.216 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.0697 time to fit residues: 1.6066 Evaluate side-chains 18 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.0020 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1870 Z= 0.181 Angle : 0.773 8.643 2540 Z= 0.376 Chirality : 0.044 0.131 300 Planarity : 0.002 0.011 330 Dihedral : 4.604 13.742 250 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 18.57 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 18 PHE 0.008 0.001 PHE E 15 TYR 0.003 0.000 TYR G 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.170 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0525 time to fit residues: 1.2828 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 40.0000 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.098269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.087746 restraints weight = 6176.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.089663 restraints weight = 3187.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.091090 restraints weight = 2013.197| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1870 Z= 0.251 Angle : 0.813 8.645 2540 Z= 0.405 Chirality : 0.044 0.133 300 Planarity : 0.002 0.011 330 Dihedral : 4.719 13.927 250 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 18.57 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 18 PHE 0.010 0.002 PHE C 15 TYR 0.005 0.001 TYR D 37 =============================================================================== Job complete usr+sys time: 632.71 seconds wall clock time: 17 minutes 13.24 seconds (1033.24 seconds total)