Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kew_37170/09_2024/8kew_37170.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kew_37170/09_2024/8kew_37170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kew_37170/09_2024/8kew_37170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kew_37170/09_2024/8kew_37170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kew_37170/09_2024/8kew_37170.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kew_37170/09_2024/8kew_37170.cif" } resolution = 3.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6 5.16 5 C 978 2.51 5 N 252 2.21 5 O 264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 1500 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Restraints were copied for chains: C, B, D, G, F Time building chain proxies: 0.91, per 1000 atoms: 0.61 Number of scatterers: 1500 At special positions: 0 Unit cell: (68.89, 68.89, 36.52, 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 6 16.00 O 264 8.00 N 252 7.00 C 978 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=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 180.3 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.392A pdb=" N VAL F 12 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 12 " --> pdb=" O HIS B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 25 removed outlier: 6.397A pdb=" N VAL F 24 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 24 " --> pdb=" O GLY B 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 30 through 36 removed outlier: 6.909A pdb=" N ILE A 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE F 32 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY A 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 31 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 32 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY B 33 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 13 removed outlier: 6.413A pdb=" N VAL G 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 17 Processing sheet with id=AA8, first strand: chain 'G' and resid 24 through 25 removed outlier: 6.410A pdb=" N VAL G 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 30 through 36 removed outlier: 6.914A pdb=" N ILE C 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE G 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY C 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE D 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE C 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY D 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 40 through 41 20 hydrogen bonds defined for protein. 60 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: 0.31 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 486 1.34 - 1.45: 181 1.45 - 1.56: 845 1.56 - 1.68: 0 1.68 - 1.79: 12 Bond restraints: 1524 Sorted by residual: bond pdb=" CG LEU F 34 " pdb=" CD1 LEU F 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CG LEU G 34 " pdb=" CD1 LEU G 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CG LEU B 34 " pdb=" CD1 LEU B 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CG LEU A 34 " pdb=" CD1 LEU A 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CG LEU C 34 " pdb=" CD1 LEU C 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 1519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 1617 0.88 - 1.75: 313 1.75 - 2.63: 80 2.63 - 3.50: 30 3.50 - 4.38: 6 Bond angle restraints: 2046 Sorted by residual: angle pdb=" N GLU C 22 " pdb=" CA GLU C 22 " pdb=" C GLU C 22 " ideal model delta sigma weight residual 108.45 112.83 -4.38 1.26e+00 6.30e-01 1.21e+01 angle pdb=" N GLU F 22 " pdb=" CA GLU F 22 " pdb=" C GLU F 22 " ideal model delta sigma weight residual 108.45 112.81 -4.36 1.26e+00 6.30e-01 1.20e+01 angle pdb=" N GLU A 22 " pdb=" CA GLU A 22 " pdb=" C GLU A 22 " ideal model delta sigma weight residual 108.45 112.81 -4.36 1.26e+00 6.30e-01 1.20e+01 angle pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" C GLU B 22 " ideal model delta sigma weight residual 108.45 112.81 -4.36 1.26e+00 6.30e-01 1.19e+01 angle pdb=" N GLU D 22 " pdb=" CA GLU D 22 " pdb=" C GLU D 22 " ideal model delta sigma weight residual 108.45 112.79 -4.34 1.26e+00 6.30e-01 1.19e+01 ... (remaining 2041 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 12.24: 708 12.24 - 24.48: 96 24.48 - 36.71: 24 36.71 - 48.95: 12 48.95 - 61.18: 6 Dihedral angle restraints: 846 sinusoidal: 306 harmonic: 540 Sorted by residual: dihedral pdb=" CA HIS F 14 " pdb=" C HIS F 14 " pdb=" N GLN F 15 " pdb=" CA GLN F 15 " ideal model delta harmonic sigma weight residual 180.00 167.19 12.81 0 5.00e+00 4.00e-02 6.56e+00 dihedral pdb=" CA HIS D 14 " pdb=" C HIS D 14 " pdb=" N GLN D 15 " pdb=" CA GLN D 15 " ideal model delta harmonic sigma weight residual 180.00 167.21 12.79 0 5.00e+00 4.00e-02 6.55e+00 dihedral pdb=" CA HIS G 14 " pdb=" C HIS G 14 " pdb=" N GLN G 15 " pdb=" CA GLN G 15 " ideal model delta harmonic sigma weight residual 180.00 167.21 12.79 0 5.00e+00 4.00e-02 6.54e+00 ... (remaining 843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 79 0.029 - 0.058: 53 0.058 - 0.087: 42 0.087 - 0.116: 24 0.116 - 0.145: 36 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA VAL F 39 " pdb=" N VAL F 39 " pdb=" C VAL F 39 " pdb=" CB VAL F 39 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL C 39 " pdb=" N VAL C 39 " pdb=" C VAL C 39 " pdb=" CB VAL C 39 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL D 39 " pdb=" N VAL D 39 " pdb=" C VAL D 39 " pdb=" CB VAL D 39 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 231 not shown) Planarity restraints: 258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.006 2.00e-02 2.50e+03 4.74e-03 3.94e-01 pdb=" CG PHE A 20 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 20 " 0.006 2.00e-02 2.50e+03 4.71e-03 3.88e-01 pdb=" CG PHE G 20 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE G 20 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 20 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 20 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 20 " 0.006 2.00e-02 2.50e+03 4.67e-03 3.82e-01 pdb=" CG PHE D 20 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE D 20 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 20 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 20 " 0.001 2.00e-02 2.50e+03 ... (remaining 255 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 585 2.89 - 3.39: 1237 3.39 - 3.89: 2379 3.89 - 4.40: 2364 4.40 - 4.90: 4769 Nonbonded interactions: 11334 Sorted by model distance: nonbonded pdb=" OD1 ASN B 27 " pdb=" N LYS B 28 " model vdw 2.387 3.120 nonbonded pdb=" OD1 ASN C 27 " pdb=" N LYS C 28 " model vdw 2.387 3.120 nonbonded pdb=" OD1 ASN D 27 " pdb=" N LYS D 28 " model vdw 2.388 3.120 nonbonded pdb=" OD1 ASN G 27 " pdb=" N LYS G 28 " model vdw 2.388 3.120 nonbonded pdb=" OD1 ASN F 27 " pdb=" N LYS F 28 " model vdw 2.388 3.120 ... (remaining 11329 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 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.180 Find NCS groups from input model: 0.060 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:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.010 0.045 1524 Z= 0.628 Angle : 0.841 4.375 2046 Z= 0.523 Chirality : 0.070 0.145 234 Planarity : 0.003 0.006 258 Dihedral : 14.456 61.184 510 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -3.87 (0.44), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.34), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 14 PHE 0.011 0.002 PHE A 20 TYR 0.001 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.175 Fit side-chains REVERT: F 22 GLU cc_start: 0.8178 (mm-30) cc_final: 0.6816 (pt0) REVERT: F 26 SER cc_start: 0.8743 (m) cc_final: 0.8178 (t) REVERT: G 22 GLU cc_start: 0.8267 (mm-30) cc_final: 0.6727 (pt0) REVERT: G 26 SER cc_start: 0.8773 (m) cc_final: 0.8178 (t) REVERT: A 10 TYR cc_start: 0.7392 (m-80) cc_final: 0.7077 (m-80) REVERT: A 26 SER cc_start: 0.8559 (m) cc_final: 0.8005 (t) REVERT: A 27 ASN cc_start: 0.8853 (t0) cc_final: 0.8608 (t0) REVERT: C 22 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7965 (mm-30) REVERT: C 26 SER cc_start: 0.8652 (m) cc_final: 0.7983 (t) REVERT: B 26 SER cc_start: 0.8779 (m) cc_final: 0.8287 (t) REVERT: D 14 HIS cc_start: 0.8287 (m90) cc_final: 0.7996 (m90) REVERT: D 26 SER cc_start: 0.8757 (m) cc_final: 0.8231 (t) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1805 time to fit residues: 6.4724 Evaluate side-chains 25 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1524 Z= 0.148 Angle : 0.459 2.301 2046 Z= 0.271 Chirality : 0.062 0.130 234 Planarity : 0.001 0.007 258 Dihedral : 4.697 11.024 204 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -3.09 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 13 PHE 0.004 0.001 PHE B 20 TYR 0.001 0.000 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.166 Fit side-chains REVERT: F 22 GLU cc_start: 0.8168 (mm-30) cc_final: 0.6914 (pt0) REVERT: F 26 SER cc_start: 0.8535 (m) cc_final: 0.7963 (t) REVERT: G 22 GLU cc_start: 0.8230 (mm-30) cc_final: 0.6872 (pt0) REVERT: G 26 SER cc_start: 0.8595 (m) cc_final: 0.8019 (t) REVERT: A 10 TYR cc_start: 0.7327 (m-80) cc_final: 0.6996 (m-80) REVERT: A 14 HIS cc_start: 0.8176 (m90) cc_final: 0.7815 (m90) REVERT: A 26 SER cc_start: 0.8254 (m) cc_final: 0.7693 (t) REVERT: C 22 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7769 (mm-30) REVERT: C 26 SER cc_start: 0.8431 (m) cc_final: 0.7806 (t) REVERT: B 26 SER cc_start: 0.8484 (m) cc_final: 0.7938 (t) REVERT: D 26 SER cc_start: 0.8471 (m) cc_final: 0.7919 (t) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0941 time to fit residues: 3.3477 Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 1.3302 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1524 Z= 0.206 Angle : 0.467 2.381 2046 Z= 0.276 Chirality : 0.062 0.140 234 Planarity : 0.001 0.006 258 Dihedral : 4.560 10.689 204 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % 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: -2.67 (0.48), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 14 PHE 0.007 0.001 PHE B 20 TYR 0.002 0.000 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.159 Fit side-chains REVERT: F 22 GLU cc_start: 0.8136 (mm-30) cc_final: 0.6813 (pt0) REVERT: F 26 SER cc_start: 0.8474 (m) cc_final: 0.7933 (t) REVERT: G 16 LYS cc_start: 0.8234 (tttt) cc_final: 0.8025 (tttm) REVERT: G 22 GLU cc_start: 0.8044 (mm-30) cc_final: 0.6867 (pt0) REVERT: G 26 SER cc_start: 0.8471 (m) cc_final: 0.7896 (t) REVERT: A 10 TYR cc_start: 0.7325 (m-80) cc_final: 0.7005 (m-80) REVERT: A 22 GLU cc_start: 0.7983 (tp30) cc_final: 0.7662 (mm-30) REVERT: A 26 SER cc_start: 0.8222 (m) cc_final: 0.7629 (t) REVERT: C 22 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7820 (mm-30) REVERT: C 26 SER cc_start: 0.8322 (m) cc_final: 0.7762 (t) REVERT: B 26 SER cc_start: 0.8442 (m) cc_final: 0.7864 (t) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0953 time to fit residues: 3.2616 Evaluate side-chains 27 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.8163 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1524 Z= 0.295 Angle : 0.531 2.955 2046 Z= 0.308 Chirality : 0.063 0.149 234 Planarity : 0.002 0.005 258 Dihedral : 4.925 11.154 204 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % 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: -2.44 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 14 PHE 0.011 0.002 PHE G 20 TYR 0.002 0.000 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.158 Fit side-chains REVERT: F 22 GLU cc_start: 0.8155 (mm-30) cc_final: 0.6801 (pt0) REVERT: F 26 SER cc_start: 0.8486 (m) cc_final: 0.7951 (t) REVERT: G 22 GLU cc_start: 0.8128 (mm-30) cc_final: 0.6864 (pt0) REVERT: G 26 SER cc_start: 0.8460 (m) cc_final: 0.7926 (t) REVERT: A 10 TYR cc_start: 0.7336 (m-80) cc_final: 0.7051 (m-80) REVERT: A 22 GLU cc_start: 0.8134 (tp30) cc_final: 0.7820 (mm-30) REVERT: A 26 SER cc_start: 0.8287 (m) cc_final: 0.7682 (t) REVERT: C 22 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 26 SER cc_start: 0.8322 (m) cc_final: 0.7742 (t) REVERT: B 26 SER cc_start: 0.8390 (m) cc_final: 0.7827 (t) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0820 time to fit residues: 2.9789 Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1524 Z= 0.145 Angle : 0.438 2.277 2046 Z= 0.256 Chirality : 0.061 0.131 234 Planarity : 0.001 0.006 258 Dihedral : 4.253 10.562 204 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 14 PHE 0.003 0.001 PHE G 20 TYR 0.001 0.000 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.170 Fit side-chains REVERT: F 22 GLU cc_start: 0.7975 (mm-30) cc_final: 0.6857 (pt0) REVERT: F 26 SER cc_start: 0.8412 (m) cc_final: 0.7812 (t) REVERT: G 16 LYS cc_start: 0.8260 (tttt) cc_final: 0.8004 (tttm) REVERT: G 26 SER cc_start: 0.8455 (m) cc_final: 0.7933 (t) REVERT: A 10 TYR cc_start: 0.7300 (m-80) cc_final: 0.7004 (m-80) REVERT: A 22 GLU cc_start: 0.8003 (tp30) cc_final: 0.7736 (mm-30) REVERT: A 26 SER cc_start: 0.8190 (m) cc_final: 0.7560 (t) REVERT: C 22 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 26 SER cc_start: 0.8176 (m) cc_final: 0.7558 (t) REVERT: B 26 SER cc_start: 0.8345 (m) cc_final: 0.7758 (t) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0919 time to fit residues: 3.2723 Evaluate side-chains 28 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1524 Z= 0.130 Angle : 0.453 3.696 2046 Z= 0.267 Chirality : 0.060 0.129 234 Planarity : 0.001 0.004 258 Dihedral : 4.062 10.942 204 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.53), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 14 PHE 0.002 0.001 PHE G 20 TYR 0.001 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.161 Fit side-chains REVERT: F 26 SER cc_start: 0.8303 (m) cc_final: 0.7733 (t) REVERT: A 10 TYR cc_start: 0.7275 (m-80) cc_final: 0.6954 (m-80) REVERT: A 22 GLU cc_start: 0.7975 (tp30) cc_final: 0.7672 (mm-30) REVERT: C 22 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 26 SER cc_start: 0.8131 (m) cc_final: 0.7485 (t) REVERT: B 22 GLU cc_start: 0.7891 (tp30) cc_final: 0.7427 (mm-30) REVERT: B 26 SER cc_start: 0.8252 (m) cc_final: 0.7683 (t) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0921 time to fit residues: 3.2803 Evaluate side-chains 27 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1524 Z= 0.241 Angle : 0.499 3.511 2046 Z= 0.292 Chirality : 0.062 0.135 234 Planarity : 0.002 0.016 258 Dihedral : 4.388 10.949 204 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 19.33 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.54), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 14 PHE 0.009 0.001 PHE G 20 TYR 0.001 0.000 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.160 Fit side-chains REVERT: F 26 SER cc_start: 0.8335 (m) cc_final: 0.7761 (t) REVERT: A 10 TYR cc_start: 0.7321 (m-80) cc_final: 0.7028 (m-80) REVERT: A 22 GLU cc_start: 0.8033 (tp30) cc_final: 0.7687 (mm-30) REVERT: C 22 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 26 SER cc_start: 0.8181 (m) cc_final: 0.7544 (t) REVERT: B 22 GLU cc_start: 0.7989 (tp30) cc_final: 0.7548 (mm-30) REVERT: B 26 SER cc_start: 0.8390 (m) cc_final: 0.7808 (t) REVERT: D 22 GLU cc_start: 0.8071 (tp30) cc_final: 0.7698 (mm-30) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0781 time to fit residues: 2.8711 Evaluate side-chains 28 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1524 Z= 0.165 Angle : 0.466 3.992 2046 Z= 0.274 Chirality : 0.061 0.136 234 Planarity : 0.001 0.016 258 Dihedral : 4.147 11.403 204 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 20.00 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 14 PHE 0.005 0.001 PHE G 20 TYR 0.001 0.000 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.166 Fit side-chains REVERT: F 26 SER cc_start: 0.8311 (m) cc_final: 0.7716 (t) REVERT: A 10 TYR cc_start: 0.7336 (m-80) cc_final: 0.7030 (m-80) REVERT: A 22 GLU cc_start: 0.7984 (tp30) cc_final: 0.7739 (mm-30) REVERT: C 22 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 26 SER cc_start: 0.8271 (m) cc_final: 0.7676 (t) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0724 time to fit residues: 2.3876 Evaluate side-chains 25 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8160 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 1524 Z= 0.384 Angle : 0.602 4.031 2046 Z= 0.349 Chirality : 0.065 0.145 234 Planarity : 0.002 0.006 258 Dihedral : 5.284 11.384 204 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.67 % Allowed : 20.00 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 14 PHE 0.015 0.002 PHE G 20 TYR 0.002 0.000 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.151 Fit side-chains REVERT: F 22 GLU cc_start: 0.8227 (mm-30) cc_final: 0.6919 (pt0) REVERT: F 26 SER cc_start: 0.8415 (m) cc_final: 0.7857 (t) REVERT: A 10 TYR cc_start: 0.7374 (m-80) cc_final: 0.7096 (m-80) REVERT: C 26 SER cc_start: 0.8192 (m) cc_final: 0.7518 (t) REVERT: B 26 SER cc_start: 0.8440 (m) cc_final: 0.7862 (t) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.0768 time to fit residues: 2.8925 Evaluate side-chains 29 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1524 Z= 0.147 Angle : 0.485 3.538 2046 Z= 0.286 Chirality : 0.061 0.136 234 Planarity : 0.001 0.004 258 Dihedral : 4.212 11.718 204 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.57), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 14 PHE 0.003 0.001 PHE B 19 TYR 0.002 0.000 TYR D 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.150 Fit side-chains REVERT: F 26 SER cc_start: 0.8320 (m) cc_final: 0.7711 (t) REVERT: A 10 TYR cc_start: 0.7346 (m-80) cc_final: 0.7053 (m-80) REVERT: A 22 GLU cc_start: 0.7954 (tp30) cc_final: 0.7657 (mm-30) REVERT: B 26 SER cc_start: 0.8340 (m) cc_final: 0.7722 (t) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0838 time to fit residues: 2.5865 Evaluate side-chains 23 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.131721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.104209 restraints weight = 1583.582| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.01 r_work: 0.3241 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1524 Z= 0.232 Angle : 0.513 3.324 2046 Z= 0.301 Chirality : 0.062 0.138 234 Planarity : 0.001 0.006 258 Dihedral : 4.369 11.322 204 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 20.67 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 14 PHE 0.005 0.001 PHE B 20 TYR 0.001 0.000 TYR D 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 936.76 seconds wall clock time: 17 minutes 1.01 seconds (1021.01 seconds total)