Starting phenix.real_space_refine on Mon Sep 23 11:46:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/09_2024/7m65_23689.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/09_2024/7m65_23689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/09_2024/7m65_23689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/09_2024/7m65_23689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/09_2024/7m65_23689.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/09_2024/7m65_23689.cif" } resolution = 4.1 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1235 2.51 5 N 370 2.21 5 O 415 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: 2025 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 237 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 1.45, per 1000 atoms: 0.72 Number of scatterers: 2025 At special positions: 0 Unit cell: (62.245, 68.575, 45.365, 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 5 16.00 O 415 8.00 N 370 7.00 C 1235 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 254.9 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 10 removed outlier: 3.604A pdb=" N THR E 9 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 9 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N CYS A 7 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLN G 10 " --> pdb=" O CYS A 7 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 9 " --> pdb=" O GLN G 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR I 9 " --> pdb=" O ALA A 8 " (cutoff:3.500A) 6 hydrogen bonds defined for protein. 18 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: 0.37 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 337 1.31 - 1.44: 613 1.44 - 1.56: 1090 1.56 - 1.68: 0 1.68 - 1.81: 5 Bond restraints: 2045 Sorted by residual: bond pdb=" CG ASN C 35 " pdb=" OD1 ASN C 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.93e+00 bond pdb=" CG ASN E 35 " pdb=" OD1 ASN E 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.78e+00 bond pdb=" CG ASN I 35 " pdb=" OD1 ASN I 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.74e+00 bond pdb=" CG ASN G 35 " pdb=" OD1 ASN G 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.59e+00 bond pdb=" CG ASN A 35 " pdb=" OD1 ASN A 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.55e+00 ... (remaining 2040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 2598 2.33 - 4.67: 132 4.67 - 7.00: 30 7.00 - 9.33: 10 9.33 - 11.66: 5 Bond angle restraints: 2775 Sorted by residual: angle pdb=" N PHE F 15 " pdb=" CA PHE F 15 " pdb=" C PHE F 15 " ideal model delta sigma weight residual 112.41 119.39 -6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" N PHE J 15 " pdb=" CA PHE J 15 " pdb=" C PHE J 15 " ideal model delta sigma weight residual 112.41 119.38 -6.97 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE B 15 " pdb=" CA PHE B 15 " pdb=" C PHE B 15 " ideal model delta sigma weight residual 112.41 119.37 -6.96 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE D 15 " pdb=" CA PHE D 15 " pdb=" C PHE D 15 " ideal model delta sigma weight residual 112.41 119.36 -6.95 1.30e+00 5.92e-01 2.86e+01 angle pdb=" N PHE H 15 " pdb=" CA PHE H 15 " pdb=" C PHE H 15 " ideal model delta sigma weight residual 112.41 119.34 -6.93 1.30e+00 5.92e-01 2.84e+01 ... (remaining 2770 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.26: 870 8.26 - 16.50: 195 16.50 - 24.75: 55 24.75 - 33.00: 35 33.00 - 41.24: 10 Dihedral angle restraints: 1165 sinusoidal: 385 harmonic: 780 Sorted by residual: dihedral pdb=" CA PHE H 15 " pdb=" C PHE H 15 " pdb=" N LEU H 16 " pdb=" CA LEU H 16 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE J 15 " pdb=" C PHE J 15 " pdb=" N LEU J 16 " pdb=" CA LEU J 16 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE D 15 " pdb=" C PHE D 15 " pdb=" N LEU D 16 " pdb=" CA LEU D 16 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 1162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 312 0.132 - 0.264: 23 0.264 - 0.396: 0 0.396 - 0.528: 0 0.528 - 0.660: 5 Chirality restraints: 340 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE J 26 " pdb=" CA ILE J 26 " pdb=" CG1 ILE J 26 " pdb=" CG2 ILE J 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 337 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.70e+00 pdb=" CG PHE E 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE E 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.69e+00 pdb=" CG PHE I 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.68e+00 pdb=" CG PHE A 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 15 " -0.003 2.00e-02 2.50e+03 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 936 2.89 - 3.40: 2346 3.40 - 3.90: 3188 3.90 - 4.40: 3720 4.40 - 4.90: 6916 Nonbonded interactions: 17106 Sorted by model distance: nonbonded pdb=" O LEU J 16 " pdb=" CD2 LEU J 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU D 16 " pdb=" CD2 LEU D 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU B 16 " pdb=" CD2 LEU B 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU F 16 " pdb=" CD2 LEU F 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU H 16 " pdb=" CD2 LEU H 16 " model vdw 2.393 3.460 ... (remaining 17101 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' 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: 0.110 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.240 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 : 0.009 0.063 2045 Z= 0.595 Angle : 1.401 11.663 2775 Z= 0.744 Chirality : 0.102 0.660 340 Planarity : 0.004 0.012 360 Dihedral : 12.046 41.242 655 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 33.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -6.09 (0.25), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.19), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS H 18 PHE 0.028 0.005 PHE E 15 TYR 0.008 0.002 TYR E 37 ARG 0.001 0.000 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.304 Fit side-chains REVERT: C 15 PHE cc_start: 0.7309 (p90) cc_final: 0.5719 (t80) REVERT: C 28 SER cc_start: 0.8833 (t) cc_final: 0.8519 (p) REVERT: E 28 SER cc_start: 0.8926 (t) cc_final: 0.8483 (p) REVERT: G 28 SER cc_start: 0.9166 (t) cc_final: 0.8770 (p) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1409 time to fit residues: 8.8040 Evaluate side-chains 34 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2045 Z= 0.237 Angle : 0.868 12.195 2775 Z= 0.410 Chirality : 0.045 0.131 340 Planarity : 0.003 0.015 360 Dihedral : 7.741 24.574 275 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % 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: -5.77 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.012 0.003 PHE J 23 TYR 0.005 0.001 TYR G 37 ARG 0.003 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.246 Fit side-chains REVERT: C 28 SER cc_start: 0.8734 (t) cc_final: 0.8529 (p) REVERT: E 27 LEU cc_start: 0.8897 (mp) cc_final: 0.8648 (mp) REVERT: G 28 SER cc_start: 0.9110 (t) cc_final: 0.8703 (p) REVERT: J 22 ASN cc_start: 0.7814 (p0) cc_final: 0.7080 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0827 time to fit residues: 4.2355 Evaluate side-chains 29 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 0.0570 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 15 optimal weight: 10.0000 overall best weight: 6.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2045 Z= 0.207 Angle : 0.749 9.452 2775 Z= 0.369 Chirality : 0.043 0.142 340 Planarity : 0.003 0.017 360 Dihedral : 7.073 22.494 275 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % 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: -5.56 (0.31), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.23), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.011 0.002 PHE J 23 TYR 0.004 0.001 TYR E 37 ARG 0.003 0.001 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.247 Fit side-chains REVERT: E 32 VAL cc_start: 0.8120 (p) cc_final: 0.7636 (p) REVERT: G 28 SER cc_start: 0.9212 (t) cc_final: 0.8855 (p) REVERT: J 22 ASN cc_start: 0.7415 (p0) cc_final: 0.7086 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0895 time to fit residues: 4.5242 Evaluate side-chains 26 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2045 Z= 0.181 Angle : 0.717 9.466 2775 Z= 0.346 Chirality : 0.043 0.145 340 Planarity : 0.002 0.014 360 Dihedral : 6.713 20.709 275 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % 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: -5.62 (0.30), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.23), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 18 PHE 0.011 0.002 PHE G 15 TYR 0.002 0.001 TYR E 37 ARG 0.003 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: E 10 GLN cc_start: 0.7901 (mp10) cc_final: 0.7672 (mp10) REVERT: J 22 ASN cc_start: 0.7405 (p0) cc_final: 0.7015 (t0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0948 time to fit residues: 4.7387 Evaluate side-chains 26 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS E 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2045 Z= 0.238 Angle : 0.705 9.989 2775 Z= 0.354 Chirality : 0.042 0.141 340 Planarity : 0.003 0.018 360 Dihedral : 6.993 20.652 275 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -5.89 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 18 PHE 0.013 0.003 PHE H 15 TYR 0.004 0.001 TYR E 37 ARG 0.003 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.258 Fit side-chains REVERT: E 10 GLN cc_start: 0.7859 (mp10) cc_final: 0.7554 (mp10) REVERT: J 22 ASN cc_start: 0.7862 (p0) cc_final: 0.6777 (t0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0681 time to fit residues: 2.9245 Evaluate side-chains 24 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 0.0980 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 HIS I 18 HIS I 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2045 Z= 0.158 Angle : 0.752 10.897 2775 Z= 0.338 Chirality : 0.044 0.136 340 Planarity : 0.002 0.011 360 Dihedral : 6.297 19.581 275 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -5.66 (0.29), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 18 PHE 0.012 0.002 PHE D 15 TYR 0.002 0.000 TYR E 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.223 Fit side-chains REVERT: J 22 ASN cc_start: 0.7388 (p0) cc_final: 0.6603 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0763 time to fit residues: 4.0679 Evaluate side-chains 23 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 15 optimal weight: 50.0000 chunk 16 optimal weight: 40.0000 chunk 11 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 40.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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: 0.7279 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2045 Z= 0.297 Angle : 0.814 10.737 2775 Z= 0.399 Chirality : 0.046 0.154 340 Planarity : 0.003 0.021 360 Dihedral : 7.283 19.732 275 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: -5.98 (0.26), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 18 PHE 0.015 0.003 PHE E 15 TYR 0.003 0.001 TYR E 37 ARG 0.004 0.001 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0631 time to fit residues: 2.7358 Evaluate side-chains 22 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2045 Z= 0.196 Angle : 0.791 10.379 2775 Z= 0.366 Chirality : 0.045 0.152 340 Planarity : 0.002 0.013 360 Dihedral : 6.712 19.279 275 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -5.82 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.013 0.002 PHE D 15 TYR 0.003 0.001 TYR E 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0612 time to fit residues: 2.6688 Evaluate side-chains 25 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 overall best weight: 11.1996 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2045 Z= 0.315 Angle : 0.817 10.707 2775 Z= 0.397 Chirality : 0.045 0.177 340 Planarity : 0.003 0.020 360 Dihedral : 7.364 20.623 275 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -6.05 (0.26), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 18 PHE 0.018 0.003 PHE H 15 TYR 0.004 0.001 TYR E 37 ARG 0.003 0.001 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0506 time to fit residues: 1.9545 Evaluate side-chains 22 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2045 Z= 0.228 Angle : 0.757 10.815 2775 Z= 0.364 Chirality : 0.044 0.157 340 Planarity : 0.003 0.015 360 Dihedral : 7.018 19.562 275 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -6.04 (0.25), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.19), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.015 0.003 PHE E 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.001 ARG I 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0616 time to fit residues: 2.3889 Evaluate side-chains 23 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 40.0000 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.096844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.088952 restraints weight = 10029.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.090702 restraints weight = 5023.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.091836 restraints weight = 2989.040| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2045 Z= 0.252 Angle : 0.771 10.362 2775 Z= 0.373 Chirality : 0.045 0.163 340 Planarity : 0.003 0.015 360 Dihedral : 7.033 19.805 275 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.47 % Favored : 83.53 % 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: -6.04 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.60 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.014 0.003 PHE E 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.001 ARG I 11 =============================================================================== Job complete usr+sys time: 710.60 seconds wall clock time: 19 minutes 1.64 seconds (1141.64 seconds total)