Starting phenix.real_space_refine on Sun Mar 10 15:10:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjx_33236/03_2024/7xjx_33236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjx_33236/03_2024/7xjx_33236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjx_33236/03_2024/7xjx_33236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjx_33236/03_2024/7xjx_33236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjx_33236/03_2024/7xjx_33236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjx_33236/03_2024/7xjx_33236.pdb" } resolution = 2.7 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 1.80, per 1000 atoms: 0.68 Number of scatterers: 2628 At special positions: 0 Unit cell: (108.272, 95.408, 31.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 528 8.00 N 456 7.00 C 1644 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 - 3.50 Amino acid : False - 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: 0.90 Conformation dependent library (CDL) restraints added in 580.0 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 46 through 56 removed outlier: 7.570A pdb=" N GLY B 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N HIS E 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N VAL B 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N VAL E 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY B 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR E 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA E 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL F 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS B 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY F 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 60 through 65 removed outlier: 6.476A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 71 through 78 removed outlier: 6.417A pdb=" N THR B 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR E 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL E 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA B 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR F 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA F 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 56 removed outlier: 7.551A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N HIS C 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS A 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY D 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 65 removed outlier: 6.490A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 78 removed outlier: 6.408A pdb=" N THR A 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR C 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA D 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 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: 0.50 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 462 1.28 - 1.35: 408 1.35 - 1.41: 99 1.41 - 1.48: 441 1.48 - 1.54: 1230 Bond restraints: 2640 Sorted by residual: bond pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.25e+00 bond pdb=" CA GLY C 68 " pdb=" C GLY C 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.24e+00 bond pdb=" CA GLY B 68 " pdb=" C GLY B 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.23e+00 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.19e+00 bond pdb=" CA GLY E 68 " pdb=" C GLY E 68 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.14e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 104.36 - 109.74: 372 109.74 - 115.13: 1422 115.13 - 120.51: 706 120.51 - 125.90: 1064 125.90 - 131.29: 6 Bond angle restraints: 3570 Sorted by residual: angle pdb=" N HIS E 50 " pdb=" CA HIS E 50 " pdb=" C HIS E 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.16e+00 angle pdb=" N HIS B 50 " pdb=" CA HIS B 50 " pdb=" C HIS B 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.16e+00 angle pdb=" N HIS C 50 " pdb=" CA HIS C 50 " pdb=" C HIS C 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.15e+00 angle pdb=" N HIS F 50 " pdb=" CA HIS F 50 " pdb=" C HIS F 50 " ideal model delta sigma weight residual 108.99 113.69 -4.70 1.57e+00 4.06e-01 8.98e+00 angle pdb=" N HIS A 50 " pdb=" CA HIS A 50 " pdb=" C HIS A 50 " ideal model delta sigma weight residual 108.99 113.69 -4.70 1.57e+00 4.06e-01 8.95e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.68: 1206 9.68 - 19.36: 240 19.36 - 29.03: 60 29.03 - 38.71: 24 38.71 - 48.39: 18 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA ALA C 89 " pdb=" C ALA C 89 " pdb=" N ALA C 90 " pdb=" CA ALA C 90 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ALA E 89 " pdb=" C ALA E 89 " pdb=" N ALA E 90 " pdb=" CA ALA E 90 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ALA A 89 " pdb=" C ALA A 89 " pdb=" N ALA A 90 " pdb=" CA ALA A 90 " ideal model delta harmonic sigma weight residual 180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 243 0.036 - 0.071: 116 0.071 - 0.106: 61 0.106 - 0.141: 30 0.141 - 0.177: 18 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 48 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C VAL E 48 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL E 48 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 49 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 48 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C VAL D 48 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL D 48 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL D 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 48 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C VAL F 48 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL F 48 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL F 49 " 0.010 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1203 2.93 - 3.42: 2369 3.42 - 3.92: 3923 3.92 - 4.41: 4245 4.41 - 4.90: 9221 Nonbonded interactions: 20961 Sorted by model distance: nonbonded pdb=" O THR C 64 " pdb=" OG1 THR C 64 " model vdw 2.438 2.440 nonbonded pdb=" O THR B 64 " pdb=" OG1 THR B 64 " model vdw 2.438 2.440 nonbonded pdb=" O THR D 64 " pdb=" OG1 THR D 64 " model vdw 2.439 2.440 nonbonded pdb=" O THR A 64 " pdb=" OG1 THR A 64 " model vdw 2.439 2.440 nonbonded pdb=" O THR E 64 " pdb=" OG1 THR E 64 " model vdw 2.439 2.440 ... (remaining 20956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.100 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: 4.720 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 2640 Z= 0.548 Angle : 0.806 5.379 3570 Z= 0.484 Chirality : 0.063 0.177 468 Planarity : 0.003 0.017 444 Dihedral : 12.769 48.390 900 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.39 % Favored : 83.61 % Rotamer: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.002 0.001 PHE C 94 TYR 0.009 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.289 Fit side-chains REVERT: B 54 THR cc_start: 0.8956 (p) cc_final: 0.8731 (p) REVERT: D 60 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7814 (tttt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 1.1731 time to fit residues: 51.7838 Evaluate side-chains 39 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2640 Z= 0.130 Angle : 0.495 3.265 3570 Z= 0.286 Chirality : 0.050 0.128 468 Planarity : 0.002 0.011 444 Dihedral : 5.496 16.328 378 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 4.44 % Allowed : 21.85 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.002 0.000 PHE B 94 TYR 0.003 0.000 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.300 Fit side-chains REVERT: B 43 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7596 (mptt) REVERT: D 60 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7805 (tttt) outliers start: 12 outliers final: 4 residues processed: 43 average time/residue: 1.1766 time to fit residues: 52.0107 Evaluate side-chains 41 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.0570 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 79 GLN C 79 GLN F 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2640 Z= 0.175 Angle : 0.482 3.320 3570 Z= 0.276 Chirality : 0.050 0.125 468 Planarity : 0.002 0.008 444 Dihedral : 5.439 16.593 378 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 7.04 % Allowed : 17.41 % Favored : 75.56 % 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: -3.98 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.002 0.000 PHE A 94 TYR 0.008 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 35 time to evaluate : 0.331 Fit side-chains REVERT: B 43 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7947 (mptt) outliers start: 19 outliers final: 10 residues processed: 48 average time/residue: 1.0016 time to fit residues: 49.5016 Evaluate side-chains 45 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2640 Z= 0.349 Angle : 0.602 3.874 3570 Z= 0.340 Chirality : 0.052 0.130 468 Planarity : 0.002 0.012 444 Dihedral : 6.407 19.535 378 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 5.93 % Allowed : 18.52 % Favored : 75.56 % 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: -3.90 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 50 PHE 0.004 0.001 PHE C 94 TYR 0.011 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.258 Fit side-chains REVERT: B 43 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7677 (mptt) outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 1.0652 time to fit residues: 49.3170 Evaluate side-chains 49 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 35 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2640 Z= 0.401 Angle : 0.637 3.759 3570 Z= 0.359 Chirality : 0.053 0.129 468 Planarity : 0.003 0.013 444 Dihedral : 6.747 21.032 378 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 6.30 % Allowed : 18.52 % Favored : 75.19 % 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: -3.88 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS B 50 PHE 0.005 0.001 PHE C 94 TYR 0.010 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 37 time to evaluate : 0.306 Fit side-chains REVERT: B 43 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7724 (mptt) REVERT: E 83 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6707 (tm-30) REVERT: C 43 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7772 (mmtp) REVERT: F 83 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6617 (tm-30) outliers start: 17 outliers final: 14 residues processed: 47 average time/residue: 1.1013 time to fit residues: 53.1958 Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 0.020 2640 Z= 0.158 Angle : 0.517 5.434 3570 Z= 0.293 Chirality : 0.050 0.126 468 Planarity : 0.002 0.010 444 Dihedral : 5.757 18.490 378 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 5.93 % Allowed : 19.26 % Favored : 74.81 % 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: -3.72 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.001 0.000 PHE C 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.300 Fit side-chains REVERT: B 43 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7837 (mptt) outliers start: 16 outliers final: 12 residues processed: 46 average time/residue: 1.1492 time to fit residues: 54.3082 Evaluate side-chains 46 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2640 Z= 0.283 Angle : 0.597 6.525 3570 Z= 0.333 Chirality : 0.050 0.123 468 Planarity : 0.002 0.008 444 Dihedral : 6.210 20.723 378 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.03 % Favored : 84.97 % Rotamer: Outliers : 5.56 % Allowed : 19.63 % Favored : 74.81 % 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: -3.67 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS B 50 PHE 0.004 0.001 PHE C 94 TYR 0.009 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.269 Fit side-chains REVERT: B 43 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7719 (mptt) REVERT: E 83 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6734 (tm-30) REVERT: F 83 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6684 (tm-30) outliers start: 15 outliers final: 12 residues processed: 50 average time/residue: 1.0808 time to fit residues: 55.5157 Evaluate side-chains 50 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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: 0.7760 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2640 Z= 0.270 Angle : 0.608 7.480 3570 Z= 0.337 Chirality : 0.051 0.124 468 Planarity : 0.002 0.008 444 Dihedral : 6.255 20.597 378 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 5.19 % Allowed : 21.11 % Favored : 73.70 % 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: -3.68 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.003 0.001 PHE C 94 TYR 0.009 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.317 Fit side-chains REVERT: B 43 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7702 (mptt) REVERT: E 83 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6758 (tm-30) REVERT: F 83 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6691 (tm-30) outliers start: 14 outliers final: 12 residues processed: 47 average time/residue: 1.1695 time to fit residues: 56.4202 Evaluate side-chains 48 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.0040 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2640 Z= 0.299 Angle : 0.696 8.257 3570 Z= 0.379 Chirality : 0.051 0.124 468 Planarity : 0.002 0.020 444 Dihedral : 6.368 21.715 378 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.30 % Favored : 84.70 % Rotamer: Outliers : 5.93 % Allowed : 19.63 % Favored : 74.44 % 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: -3.71 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS B 50 PHE 0.004 0.001 PHE C 94 TYR 0.009 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.287 Fit side-chains REVERT: B 43 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7738 (mptt) REVERT: E 83 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6761 (tm-30) outliers start: 16 outliers final: 13 residues processed: 47 average time/residue: 1.1105 time to fit residues: 53.6794 Evaluate side-chains 48 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 34 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2640 Z= 0.211 Angle : 0.664 8.471 3570 Z= 0.361 Chirality : 0.049 0.127 468 Planarity : 0.002 0.025 444 Dihedral : 5.805 19.934 378 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 5.19 % Allowed : 20.37 % Favored : 74.44 % 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: -3.58 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.001 0.000 PHE B 94 TYR 0.005 0.001 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.292 Fit side-chains REVERT: B 43 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7801 (mptt) REVERT: E 83 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6705 (tm-30) outliers start: 14 outliers final: 12 residues processed: 51 average time/residue: 1.1104 time to fit residues: 58.1413 Evaluate side-chains 48 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.192285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.159667 restraints weight = 3200.999| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.30 r_work: 0.4120 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2640 Z= 0.250 Angle : 0.701 8.249 3570 Z= 0.378 Chirality : 0.049 0.124 468 Planarity : 0.002 0.028 444 Dihedral : 6.019 19.891 378 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 4.44 % Allowed : 21.85 % Favored : 73.70 % 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: -3.52 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.002 0.001 PHE C 94 TYR 0.007 0.001 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.43 seconds wall clock time: 28 minutes 30.15 seconds (1710.15 seconds total)