Starting phenix.real_space_refine on Mon Feb 10 19:27:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kew_37170/02_2025/8kew_37170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kew_37170/02_2025/8kew_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/cci-nas-00/data/ceres_data/8kew_37170/02_2025/8kew_37170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kew_37170/02_2025/8kew_37170.map" model { file = "/net/cci-nas-00/data/ceres_data/8kew_37170/02_2025/8kew_37170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kew_37170/02_2025/8kew_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-5592/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: 1.07, per 1000 atoms: 0.71 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: 1.15 Conformation dependent library (CDL) restraints added in 186.7 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: 0.30 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: 0.37 Time building geometry restraints manager: 1.19 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 1.230 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.160 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: 0.1954 time to fit residues: 7.0406 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.119680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090171 restraints weight = 1701.625| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.24 r_work: 0.3174 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.171 Fit side-chains REVERT: F 22 GLU cc_start: 0.8352 (mm-30) cc_final: 0.6798 (pt0) REVERT: F 26 SER cc_start: 0.8261 (m) cc_final: 0.7746 (t) REVERT: G 22 GLU cc_start: 0.8343 (mm-30) cc_final: 0.6698 (pt0) REVERT: G 26 SER cc_start: 0.8285 (m) cc_final: 0.7797 (t) REVERT: A 10 TYR cc_start: 0.7435 (m-80) cc_final: 0.7117 (m-80) REVERT: A 14 HIS cc_start: 0.8063 (m90) cc_final: 0.7626 (m90) REVERT: A 26 SER cc_start: 0.7788 (m) cc_final: 0.7302 (t) REVERT: C 22 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 26 SER cc_start: 0.7963 (m) cc_final: 0.7414 (t) REVERT: B 26 SER cc_start: 0.8169 (m) cc_final: 0.7674 (t) REVERT: D 14 HIS cc_start: 0.8206 (m90) cc_final: 0.7926 (m90) REVERT: D 26 SER cc_start: 0.8155 (m) cc_final: 0.7646 (t) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0925 time to fit residues: 3.3103 Evaluate side-chains 29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.113928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.084840 restraints weight = 1773.350| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.22 r_work: 0.3274 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1783 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= 0.391 Angle : 0.573 3.403 2046 Z= 0.335 Chirality : 0.064 0.137 234 Planarity : 0.002 0.006 258 Dihedral : 5.294 11.912 204 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.67 % Allowed : 8.67 % Favored : 90.67 % 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: -2.85 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 14 PHE 0.014 0.002 PHE B 20 TYR 0.002 0.001 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 30 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.181 Fit side-chains REVERT: F 22 GLU cc_start: 0.8407 (mm-30) cc_final: 0.6805 (pt0) REVERT: F 26 SER cc_start: 0.8367 (m) cc_final: 0.7864 (t) REVERT: G 16 LYS cc_start: 0.8395 (tttt) cc_final: 0.8120 (tttm) REVERT: G 22 GLU cc_start: 0.8362 (mm-30) cc_final: 0.6789 (pt0) REVERT: G 26 SER cc_start: 0.8315 (m) cc_final: 0.7829 (t) REVERT: A 10 TYR cc_start: 0.7516 (m-80) cc_final: 0.7247 (m-80) REVERT: A 14 HIS cc_start: 0.8096 (m90) cc_final: 0.7795 (m90) REVERT: A 22 GLU cc_start: 0.8155 (tp30) cc_final: 0.7651 (mm-30) REVERT: A 26 SER cc_start: 0.8040 (m) cc_final: 0.7505 (t) REVERT: C 26 SER cc_start: 0.8049 (m) cc_final: 0.7502 (t) REVERT: B 26 SER cc_start: 0.8280 (m) cc_final: 0.7735 (t) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.0990 time to fit residues: 3.5303 Evaluate side-chains 29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.121267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091670 restraints weight = 1685.845| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.25 r_work: 0.3373 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1524 Z= 0.142 Angle : 0.445 2.183 2046 Z= 0.263 Chirality : 0.061 0.129 234 Planarity : 0.001 0.003 258 Dihedral : 4.355 10.306 204 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 11.33 % Favored : 88.00 % 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: -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 0.001 0.001 HIS D 13 PHE 0.003 0.001 PHE B 19 TYR 0.001 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 27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.152 Fit side-chains REVERT: F 22 GLU cc_start: 0.8336 (mm-30) cc_final: 0.6807 (pt0) REVERT: F 26 SER cc_start: 0.8267 (m) cc_final: 0.7738 (t) REVERT: G 16 LYS cc_start: 0.8366 (tttt) cc_final: 0.8123 (tttm) REVERT: G 26 SER cc_start: 0.8340 (m) cc_final: 0.7886 (t) REVERT: A 10 TYR cc_start: 0.7433 (m-80) cc_final: 0.7159 (m-80) REVERT: A 22 GLU cc_start: 0.8155 (tp30) cc_final: 0.7796 (mm-30) REVERT: C 22 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7811 (mm-30) REVERT: C 26 SER cc_start: 0.7919 (m) cc_final: 0.7350 (t) REVERT: B 26 SER cc_start: 0.8092 (m) cc_final: 0.7550 (t) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0929 time to fit residues: 2.9448 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.114582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086636 restraints weight = 1781.995| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.17 r_work: 0.3286 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 1524 Z= 0.488 Angle : 0.659 4.196 2046 Z= 0.379 Chirality : 0.066 0.155 234 Planarity : 0.003 0.008 258 Dihedral : 5.771 11.937 204 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % 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: -2.16 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 14 PHE 0.018 0.003 PHE F 20 TYR 0.002 0.001 TYR D 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 32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.172 Fit side-chains REVERT: F 22 GLU cc_start: 0.8434 (mm-30) cc_final: 0.6815 (pt0) REVERT: F 26 SER cc_start: 0.8393 (m) cc_final: 0.7863 (t) REVERT: G 22 GLU cc_start: 0.8293 (mm-30) cc_final: 0.6790 (pt0) REVERT: G 26 SER cc_start: 0.8383 (m) cc_final: 0.7932 (t) REVERT: G 31 ILE cc_start: 0.8738 (mt) cc_final: 0.8486 (mt) REVERT: A 10 TYR cc_start: 0.7524 (m-80) cc_final: 0.7274 (m-80) REVERT: C 26 SER cc_start: 0.8068 (m) cc_final: 0.7505 (t) REVERT: B 26 SER cc_start: 0.8235 (m) cc_final: 0.7707 (t) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0869 time to fit residues: 3.4869 Evaluate side-chains 30 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.120901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090767 restraints weight = 1754.345| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.35 r_work: 0.3379 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1524 Z= 0.210 Angle : 0.506 3.221 2046 Z= 0.294 Chirality : 0.062 0.139 234 Planarity : 0.001 0.007 258 Dihedral : 4.725 11.401 204 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.53), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 14 PHE 0.004 0.001 PHE G 20 TYR 0.001 0.000 TYR F 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 27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.169 Fit side-chains REVERT: F 22 GLU cc_start: 0.8330 (mm-30) cc_final: 0.6789 (pt0) REVERT: F 26 SER cc_start: 0.8228 (m) cc_final: 0.7680 (t) REVERT: G 26 SER cc_start: 0.8335 (m) cc_final: 0.7841 (t) REVERT: A 10 TYR cc_start: 0.7389 (m-80) cc_final: 0.7121 (m-80) REVERT: A 22 GLU cc_start: 0.8098 (tp30) cc_final: 0.7525 (mm-30) REVERT: B 22 GLU cc_start: 0.8152 (tp30) cc_final: 0.7504 (mm-30) REVERT: B 26 SER cc_start: 0.8113 (m) cc_final: 0.7575 (t) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0895 time to fit residues: 3.0225 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.115034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.085320 restraints weight = 1823.139| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.66 r_work: 0.3396 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1524 Z= 0.183 Angle : 0.469 2.698 2046 Z= 0.273 Chirality : 0.061 0.139 234 Planarity : 0.001 0.006 258 Dihedral : 4.461 12.770 204 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 17.33 % Favored : 82.67 % 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: -1.33 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.003 0.001 PHE C 20 TYR 0.001 0.000 TYR F 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 27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.200 Fit side-chains REVERT: F 14 HIS cc_start: 0.8377 (m90) cc_final: 0.8174 (m90) REVERT: F 22 GLU cc_start: 0.8300 (mm-30) cc_final: 0.6846 (pt0) REVERT: F 26 SER cc_start: 0.8237 (m) cc_final: 0.7674 (t) REVERT: G 26 SER cc_start: 0.8283 (m) cc_final: 0.7775 (t) REVERT: A 22 GLU cc_start: 0.8093 (tp30) cc_final: 0.7667 (mm-30) REVERT: B 22 GLU cc_start: 0.8096 (tp30) cc_final: 0.7538 (mm-30) REVERT: B 23 ASP cc_start: 0.7143 (t70) cc_final: 0.6940 (t0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0914 time to fit residues: 3.2423 Evaluate side-chains 26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.105823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078825 restraints weight = 1943.727| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.38 r_work: 0.3311 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 1524 Z= 0.416 Angle : 0.632 4.467 2046 Z= 0.366 Chirality : 0.066 0.160 234 Planarity : 0.003 0.009 258 Dihedral : 5.374 13.894 204 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 14 PHE 0.015 0.002 PHE G 20 TYR 0.011 0.001 TYR A 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 27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.172 Fit side-chains REVERT: F 14 HIS cc_start: 0.8369 (m90) cc_final: 0.8168 (m90) REVERT: F 22 GLU cc_start: 0.8371 (mm-30) cc_final: 0.6833 (pt0) REVERT: F 26 SER cc_start: 0.8297 (m) cc_final: 0.7738 (t) REVERT: G 26 SER cc_start: 0.8366 (m) cc_final: 0.7899 (t) REVERT: G 27 ASN cc_start: 0.8524 (t0) cc_final: 0.8308 (t0) REVERT: G 31 ILE cc_start: 0.8753 (mt) cc_final: 0.8500 (mt) REVERT: A 22 GLU cc_start: 0.8139 (tp30) cc_final: 0.7670 (mm-30) REVERT: B 22 GLU cc_start: 0.8264 (tp30) cc_final: 0.7937 (tp30) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0892 time to fit residues: 3.0261 Evaluate side-chains 26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.119388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089724 restraints weight = 1754.570| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.30 r_work: 0.3207 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 1524 Z= 0.334 Angle : 0.580 3.820 2046 Z= 0.335 Chirality : 0.064 0.153 234 Planarity : 0.002 0.010 258 Dihedral : 5.144 15.715 204 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.009 0.001 PHE G 20 TYR 0.009 0.001 TYR A 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 28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.168 Fit side-chains REVERT: F 22 GLU cc_start: 0.8390 (mm-30) cc_final: 0.6821 (pt0) REVERT: F 26 SER cc_start: 0.8162 (m) cc_final: 0.7620 (t) REVERT: G 26 SER cc_start: 0.8205 (m) cc_final: 0.7754 (t) REVERT: G 27 ASN cc_start: 0.8432 (t0) cc_final: 0.8225 (t0) REVERT: G 31 ILE cc_start: 0.8753 (mt) cc_final: 0.8523 (mt) REVERT: A 22 GLU cc_start: 0.8065 (tp30) cc_final: 0.7604 (mm-30) REVERT: B 22 GLU cc_start: 0.8248 (tp30) cc_final: 0.7942 (tp30) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1319 time to fit residues: 4.2896 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.122364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092555 restraints weight = 1741.072| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.32 r_work: 0.3249 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1524 Z= 0.255 Angle : 0.532 3.779 2046 Z= 0.308 Chirality : 0.063 0.149 234 Planarity : 0.002 0.009 258 Dihedral : 4.831 15.049 204 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.57), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.005 0.001 PHE G 20 TYR 0.009 0.001 TYR A 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 27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.179 Fit side-chains REVERT: F 22 GLU cc_start: 0.8406 (mm-30) cc_final: 0.6840 (pt0) REVERT: F 26 SER cc_start: 0.8167 (m) cc_final: 0.7613 (t) REVERT: G 26 SER cc_start: 0.8153 (m) cc_final: 0.7690 (t) REVERT: G 31 ILE cc_start: 0.8758 (mt) cc_final: 0.8541 (mt) REVERT: A 22 GLU cc_start: 0.8039 (tp30) cc_final: 0.7656 (mm-30) REVERT: C 22 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 22 GLU cc_start: 0.8206 (tp30) cc_final: 0.7858 (tp30) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1157 time to fit residues: 3.8011 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.112046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084544 restraints weight = 1993.660| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.54 r_work: 0.3406 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1524 Z= 0.176 Angle : 0.501 3.702 2046 Z= 0.292 Chirality : 0.062 0.144 234 Planarity : 0.002 0.015 258 Dihedral : 4.458 14.307 204 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.57), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 14 PHE 0.003 0.001 PHE C 20 TYR 0.009 0.001 TYR A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1273.02 seconds wall clock time: 23 minutes 13.49 seconds (1393.49 seconds total)