Starting phenix.real_space_refine on Wed Nov 13 23:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/11_2024/8ot1_17166.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/11_2024/8ot1_17166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/11_2024/8ot1_17166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/11_2024/8ot1_17166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/11_2024/8ot1_17166.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot1_17166/11_2024/8ot1_17166.cif" } resolution = 2.59 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= 0.001 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 12 5.16 5 C 1596 2.51 5 N 432 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 1.59, per 1000 atoms: 0.65 Number of scatterers: 2460 At special positions: 0 Unit cell: (77.522, 83.126, 43.898, 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 12 16.00 O 420 8.00 N 432 7.00 C 1596 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: 0.54 Conformation dependent library (CDL) restraints added in 305.1 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 24 removed outlier: 6.384A pdb=" N LYS A 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS I 16 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE K 19 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL I 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA K 21 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE I 20 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP K 23 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU I 22 " --> pdb=" O ASP K 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 24 removed outlier: 6.384A pdb=" N LYS B 16 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS J 16 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE L 19 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL J 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA L 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE J 20 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP L 23 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU J 22 " --> pdb=" O ASP L 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds 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: 0.05 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 540 1.33 - 1.45: 492 1.45 - 1.57: 1440 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 2496 Sorted by residual: bond pdb=" CA GLY A 33 " pdb=" C GLY A 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" CA GLY B 33 " pdb=" C GLY B 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" CA GLY I 33 " pdb=" C GLY I 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.51e+01 bond pdb=" CA GLY J 33 " pdb=" C GLY J 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.51e+01 bond pdb=" CA GLY D 33 " pdb=" C GLY D 33 " ideal model delta sigma weight residual 1.514 1.460 0.054 1.41e-02 5.03e+03 1.49e+01 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 2280 2.34 - 4.68: 940 4.68 - 7.01: 80 7.01 - 9.35: 24 9.35 - 11.69: 12 Bond angle restraints: 3336 Sorted by residual: angle pdb=" CA GLY F 38 " pdb=" C GLY F 38 " pdb=" O GLY F 38 " ideal model delta sigma weight residual 122.23 118.11 4.12 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY E 38 " pdb=" C GLY E 38 " pdb=" O GLY E 38 " ideal model delta sigma weight residual 122.23 118.11 4.12 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY H 38 " pdb=" C GLY H 38 " pdb=" O GLY H 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY G 38 " pdb=" C GLY G 38 " pdb=" O GLY G 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY L 38 " pdb=" C GLY L 38 " pdb=" O GLY L 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.55e+01 ... (remaining 3331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.97: 1152 12.97 - 25.93: 156 25.93 - 38.90: 24 38.90 - 51.86: 36 51.86 - 64.83: 24 Dihedral angle restraints: 1392 sinusoidal: 516 harmonic: 876 Sorted by residual: dihedral pdb=" CA GLU K 22 " pdb=" CB GLU K 22 " pdb=" CG GLU K 22 " pdb=" CD GLU K 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.23 58.23 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU L 22 " pdb=" CB GLU L 22 " pdb=" CG GLU L 22 " pdb=" CD GLU L 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.23 58.23 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU I 22 " pdb=" CB GLU I 22 " pdb=" CG GLU I 22 " pdb=" CD GLU I 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.22 58.22 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.053: 84 0.053 - 0.104: 60 0.104 - 0.155: 132 0.155 - 0.207: 84 0.207 - 0.258: 24 Chirality restraints: 384 Sorted by residual: chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE L 31 " pdb=" N ILE L 31 " pdb=" C ILE L 31 " pdb=" CB ILE L 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 381 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 34 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU G 34 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU G 34 " -0.021 2.00e-02 2.50e+03 pdb=" N MET G 35 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 34 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU H 34 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU H 34 " 0.021 2.00e-02 2.50e+03 pdb=" N MET H 35 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 34 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU K 34 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU K 34 " -0.021 2.00e-02 2.50e+03 pdb=" N MET K 35 " -0.019 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1042 2.96 - 3.45: 2198 3.45 - 3.93: 4190 3.93 - 4.41: 4504 4.41 - 4.90: 8910 Nonbonded interactions: 20844 Sorted by model distance: nonbonded pdb=" N LEU B 34 " pdb=" O LEU B 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU A 34 " pdb=" O LEU A 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU L 34 " pdb=" O LEU L 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU K 34 " pdb=" O LEU K 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU E 34 " pdb=" O LEU E 34 " model vdw 2.477 2.496 ... (remaining 20839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 10.070 Find NCS groups from input model: 0.110 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 : 0.013 0.055 2496 Z= 0.995 Angle : 2.400 11.686 3336 Z= 1.683 Chirality : 0.128 0.258 384 Planarity : 0.012 0.032 420 Dihedral : 17.351 64.826 840 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.27), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.021 0.005 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6951 time to fit residues: 56.2036 Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS D 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2496 Z= 0.145 Angle : 0.652 3.466 3336 Z= 0.368 Chirality : 0.052 0.121 384 Planarity : 0.003 0.016 420 Dihedral : 4.392 11.601 324 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.35 % Allowed : 31.75 % Favored : 61.90 % 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: -3.15 (0.28), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 14 PHE 0.009 0.002 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.292 Fit side-chains REVERT: E 35 MET cc_start: 0.6486 (mtp) cc_final: 0.6104 (mtt) REVERT: F 35 MET cc_start: 0.6487 (mtp) cc_final: 0.6106 (mtt) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.7531 time to fit residues: 54.6491 Evaluate side-chains 70 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.6621 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2496 Z= 0.162 Angle : 0.672 4.358 3336 Z= 0.370 Chirality : 0.051 0.125 384 Planarity : 0.003 0.013 420 Dihedral : 4.643 12.254 324 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.35 % Allowed : 22.22 % Favored : 71.43 % 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: -2.37 (0.36), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 14 PHE 0.009 0.002 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.307 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 76 average time/residue: 0.7243 time to fit residues: 57.1007 Evaluate side-chains 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.6692 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2496 Z= 0.217 Angle : 0.736 4.974 3336 Z= 0.399 Chirality : 0.051 0.138 384 Planarity : 0.003 0.012 420 Dihedral : 5.119 12.601 324 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 8.73 % Allowed : 17.46 % Favored : 73.81 % 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: -2.23 (0.37), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 14 PHE 0.011 0.002 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.285 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 78 average time/residue: 0.6845 time to fit residues: 55.4414 Evaluate side-chains 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain L residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.6600 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2496 Z= 0.115 Angle : 0.649 5.787 3336 Z= 0.349 Chirality : 0.051 0.126 384 Planarity : 0.003 0.014 420 Dihedral : 4.535 10.382 324 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.35 % Allowed : 20.63 % Favored : 73.02 % 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: -1.89 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 14 PHE 0.007 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.296 Fit side-chains REVERT: E 35 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6180 (mtt) REVERT: F 35 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6184 (mtt) REVERT: G 35 MET cc_start: 0.6828 (mtp) cc_final: 0.6401 (mtt) REVERT: H 35 MET cc_start: 0.6828 (mtp) cc_final: 0.6397 (mtt) outliers start: 16 outliers final: 6 residues processed: 74 average time/residue: 0.7110 time to fit residues: 54.5860 Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.6657 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2496 Z= 0.170 Angle : 0.715 5.856 3336 Z= 0.381 Chirality : 0.051 0.135 384 Planarity : 0.003 0.021 420 Dihedral : 4.718 11.140 324 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.56 % Allowed : 22.22 % Favored : 72.22 % 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 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 14 PHE 0.010 0.002 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.269 Fit side-chains REVERT: E 35 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6263 (mtt) REVERT: F 35 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6269 (mtt) REVERT: G 35 MET cc_start: 0.6678 (mtp) cc_final: 0.6411 (mtt) REVERT: H 35 MET cc_start: 0.6680 (mtp) cc_final: 0.6411 (mtt) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.6872 time to fit residues: 54.2310 Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.6634 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2496 Z= 0.143 Angle : 0.738 6.683 3336 Z= 0.390 Chirality : 0.053 0.131 384 Planarity : 0.003 0.020 420 Dihedral : 4.661 10.304 324 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.97 % Allowed : 23.81 % Favored : 72.22 % 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: -1.89 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 14 PHE 0.008 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.299 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.7319 time to fit residues: 53.0860 Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.6644 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2496 Z= 0.170 Angle : 0.787 7.042 3336 Z= 0.415 Chirality : 0.053 0.134 384 Planarity : 0.004 0.027 420 Dihedral : 4.775 10.696 324 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.37 % Allowed : 27.38 % Favored : 68.25 % 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: -1.90 (0.42), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 14 PHE 0.009 0.002 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.301 Fit side-chains REVERT: G 35 MET cc_start: 0.6692 (mtp) cc_final: 0.6387 (mtt) REVERT: H 35 MET cc_start: 0.6721 (mtp) cc_final: 0.6402 (mtt) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.7368 time to fit residues: 53.4862 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 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: 0.6624 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2496 Z= 0.152 Angle : 0.828 7.306 3336 Z= 0.435 Chirality : 0.053 0.131 384 Planarity : 0.004 0.029 420 Dihedral : 4.712 10.857 324 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.78 % Allowed : 28.97 % Favored : 68.25 % 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: -1.80 (0.42), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 14 PHE 0.007 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.299 Fit side-chains REVERT: G 35 MET cc_start: 0.6630 (mtp) cc_final: 0.6368 (mtt) REVERT: H 35 MET cc_start: 0.6671 (mtp) cc_final: 0.6403 (mtt) outliers start: 7 outliers final: 6 residues processed: 69 average time/residue: 0.7139 time to fit residues: 51.1522 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 21 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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: 0.6591 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2496 Z= 0.144 Angle : 0.832 7.952 3336 Z= 0.434 Chirality : 0.053 0.128 384 Planarity : 0.004 0.030 420 Dihedral : 4.612 10.684 324 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.38 % Allowed : 29.37 % Favored : 68.25 % 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: -1.76 (0.43), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 14 PHE 0.005 0.001 PHE D 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.286 Fit side-chains REVERT: G 35 MET cc_start: 0.6610 (mtp) cc_final: 0.6360 (mtt) REVERT: H 35 MET cc_start: 0.6672 (mtp) cc_final: 0.6414 (mtt) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.7273 time to fit residues: 51.2860 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.5251 r_free = 0.5251 target = 0.194738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.165928 restraints weight = 2990.917| |-----------------------------------------------------------------------------| r_work (start): 0.4968 rms_B_bonded: 3.70 r_work: 0.4876 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2496 Z= 0.164 Angle : 0.879 8.010 3336 Z= 0.457 Chirality : 0.053 0.131 384 Planarity : 0.004 0.029 420 Dihedral : 4.709 10.834 324 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.78 % Allowed : 29.76 % Favored : 67.46 % 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: -1.78 (0.42), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.007 0.001 PHE C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.69 seconds wall clock time: 30 minutes 40.20 seconds (1840.20 seconds total)