Starting phenix.real_space_refine on Mon Sep 23 16:21:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/09_2024/7ozh_13124.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/09_2024/7ozh_13124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/09_2024/7ozh_13124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/09_2024/7ozh_13124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/09_2024/7ozh_13124.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/09_2024/7ozh_13124.cif" } resolution = 3.02 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= 1.002 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 2410 2.51 5 N 680 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3890 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N LYS A 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS A 45 " occ=0.50 residue: pdb=" N LYS B 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS B 45 " occ=0.50 residue: pdb=" N LYS C 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS C 45 " occ=0.50 residue: pdb=" N LYS D 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS D 45 " occ=0.50 residue: pdb=" N LYS E 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS E 45 " occ=0.50 residue: pdb=" N LYS F 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS F 45 " occ=0.50 residue: pdb=" N LYS G 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS G 45 " occ=0.50 residue: pdb=" N LYS H 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS H 45 " occ=0.50 residue: pdb=" N LYS I 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS I 45 " occ=0.50 residue: pdb=" N LYS J 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS J 45 " occ=0.50 Time building chain proxies: 1.66, per 1000 atoms: 0.43 Number of scatterers: 3890 At special positions: 0 Unit cell: (116.55, 76.65, 43.05, 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 800 8.00 N 680 7.00 C 2410 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: 0.93 Conformation dependent library (CDL) restraints added in 520.2 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.247A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY C 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY E 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY G 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.507A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL G 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.845A pdb=" N THR A 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR C 75 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA E 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 75 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA G 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR G 75 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA I 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.404A pdb=" N ILE A 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE E 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE G 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.246A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY F 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY H 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.509A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL H 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 76 removed outlier: 6.846A pdb=" N THR B 75 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR D 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA F 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR F 75 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA H 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR H 75 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA J 76 " --> pdb=" O THR H 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.404A pdb=" N ILE B 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE F 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE H 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 56 hydrogen bonds defined for protein. 168 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: 0.86 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 690 1.28 - 1.35: 630 1.35 - 1.43: 269 1.43 - 1.51: 1434 1.51 - 1.58: 877 Bond restraints: 3900 Sorted by residual: bond pdb=" CA LYS D 45 " pdb=" CB LYS D 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.95e+01 bond pdb=" CA LYS H 45 " pdb=" CB LYS H 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.94e+01 bond pdb=" CA LYS E 45 " pdb=" CB LYS E 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.93e+01 bond pdb=" CA LYS J 45 " pdb=" CB LYS J 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.93e+01 bond pdb=" CA LYS G 45 " pdb=" CB LYS G 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.93e+01 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 3878 1.27 - 2.54: 1007 2.54 - 3.81: 285 3.81 - 5.07: 80 5.07 - 6.34: 40 Bond angle restraints: 5290 Sorted by residual: angle pdb=" C VAL A 52 " pdb=" CA VAL A 52 " pdb=" CB VAL A 52 " ideal model delta sigma weight residual 111.19 105.91 5.28 1.39e+00 5.18e-01 1.44e+01 angle pdb=" C VAL F 52 " pdb=" CA VAL F 52 " pdb=" CB VAL F 52 " ideal model delta sigma weight residual 111.19 105.93 5.26 1.39e+00 5.18e-01 1.43e+01 angle pdb=" C VAL E 52 " pdb=" CA VAL E 52 " pdb=" CB VAL E 52 " ideal model delta sigma weight residual 111.19 105.94 5.25 1.39e+00 5.18e-01 1.43e+01 angle pdb=" C VAL H 52 " pdb=" CA VAL H 52 " pdb=" CB VAL H 52 " ideal model delta sigma weight residual 111.19 105.94 5.25 1.39e+00 5.18e-01 1.43e+01 angle pdb=" C VAL J 52 " pdb=" CA VAL J 52 " pdb=" CB VAL J 52 " ideal model delta sigma weight residual 111.19 105.94 5.25 1.39e+00 5.18e-01 1.43e+01 ... (remaining 5285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.25: 1741 6.25 - 12.49: 419 12.49 - 18.73: 60 18.73 - 24.98: 20 24.98 - 31.22: 10 Dihedral angle restraints: 2250 sinusoidal: 710 harmonic: 1540 Sorted by residual: dihedral pdb=" CA GLU F 61 " pdb=" C GLU F 61 " pdb=" N GLN F 62 " pdb=" CA GLN F 62 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLU G 61 " pdb=" C GLU G 61 " pdb=" N GLN G 62 " pdb=" CA GLN G 62 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLU H 61 " pdb=" C GLU H 61 " pdb=" N GLN H 62 " pdb=" CA GLN H 62 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 260 0.045 - 0.089: 241 0.089 - 0.134: 99 0.134 - 0.178: 71 0.178 - 0.222: 39 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB VAL H 49 " pdb=" CA VAL H 49 " pdb=" CG1 VAL H 49 " pdb=" CG2 VAL H 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL C 49 " pdb=" CA VAL C 49 " pdb=" CG1 VAL C 49 " pdb=" CG2 VAL C 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL G 49 " pdb=" CA VAL G 49 " pdb=" CG1 VAL G 49 " pdb=" CG2 VAL G 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 707 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 81 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C THR B 81 " 0.048 2.00e-02 2.50e+03 pdb=" O THR B 81 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL B 82 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 81 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C THR C 81 " -0.048 2.00e-02 2.50e+03 pdb=" O THR C 81 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 82 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 81 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C THR I 81 " -0.048 2.00e-02 2.50e+03 pdb=" O THR I 81 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL I 82 " 0.016 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 2504 3.02 - 3.49: 4006 3.49 - 3.96: 5893 3.96 - 4.43: 6914 4.43 - 4.90: 13870 Nonbonded interactions: 33187 Sorted by model distance: nonbonded pdb=" N VAL A 82 " pdb=" O THR C 81 " model vdw 2.546 3.120 nonbonded pdb=" N VAL C 82 " pdb=" O THR E 81 " model vdw 2.546 3.120 nonbonded pdb=" N VAL E 82 " pdb=" O THR G 81 " model vdw 2.547 3.120 nonbonded pdb=" N VAL B 82 " pdb=" O THR D 81 " model vdw 2.547 3.120 nonbonded pdb=" N VAL H 82 " pdb=" O THR J 81 " model vdw 2.547 3.120 ... (remaining 33182 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' } 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=0.50 max=1.00 mean=0.99 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: 1.190 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.270 Find NCS groups from input model: 0.140 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 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 : 0.024 0.101 3900 Z= 1.627 Angle : 1.403 6.343 5290 Z= 0.831 Chirality : 0.088 0.222 710 Planarity : 0.008 0.028 660 Dihedral : 7.442 31.218 1290 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.26), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.20), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS B 50 TYR 0.027 0.011 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.389 Fit side-chains REVERT: A 80 LYS cc_start: 0.7607 (tttt) cc_final: 0.7045 (pttm) REVERT: B 80 LYS cc_start: 0.7372 (tttt) cc_final: 0.6660 (tmmt) REVERT: C 65 ASN cc_start: 0.6524 (m-40) cc_final: 0.6315 (m-40) REVERT: E 65 ASN cc_start: 0.6603 (m-40) cc_final: 0.6356 (m-40) REVERT: F 65 ASN cc_start: 0.6373 (m-40) cc_final: 0.5989 (m-40) REVERT: G 57 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6108 (mp0) REVERT: G 65 ASN cc_start: 0.6459 (m-40) cc_final: 0.6230 (m110) REVERT: I 50 HIS cc_start: 0.6096 (m-70) cc_final: 0.5799 (p90) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1256 time to fit residues: 15.7987 Evaluate side-chains 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3900 Z= 0.460 Angle : 0.832 5.385 5290 Z= 0.476 Chirality : 0.053 0.191 710 Planarity : 0.003 0.014 660 Dihedral : 6.586 22.028 580 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.08 % Allowed : 6.41 % Favored : 90.51 % 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: -2.03 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 TYR 0.013 0.003 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7465 (tttt) cc_final: 0.6771 (pttp) REVERT: B 80 LYS cc_start: 0.7385 (tttt) cc_final: 0.6561 (pttm) REVERT: E 80 LYS cc_start: 0.7106 (tttt) cc_final: 0.6534 (tttp) REVERT: H 39 TYR cc_start: 0.7500 (t80) cc_final: 0.7140 (t80) REVERT: H 81 THR cc_start: 0.6914 (p) cc_final: 0.6710 (p) REVERT: I 80 LYS cc_start: 0.7294 (tptm) cc_final: 0.7060 (tptm) outliers start: 12 outliers final: 10 residues processed: 122 average time/residue: 0.1539 time to fit residues: 23.3149 Evaluate side-chains 103 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3900 Z= 0.288 Angle : 0.656 4.951 5290 Z= 0.385 Chirality : 0.051 0.179 710 Planarity : 0.003 0.013 660 Dihedral : 5.919 18.308 580 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.10 % Allowed : 11.28 % Favored : 84.62 % 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: -2.07 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 50 TYR 0.009 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.383 Fit side-chains REVERT: A 80 LYS cc_start: 0.7367 (tttt) cc_final: 0.6679 (pttp) REVERT: B 80 LYS cc_start: 0.7383 (tttt) cc_final: 0.6711 (pttp) REVERT: E 80 LYS cc_start: 0.7167 (tttt) cc_final: 0.6470 (tppt) outliers start: 16 outliers final: 13 residues processed: 113 average time/residue: 0.1229 time to fit residues: 17.8690 Evaluate side-chains 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3900 Z= 0.233 Angle : 0.590 4.879 5290 Z= 0.350 Chirality : 0.051 0.174 710 Planarity : 0.002 0.011 660 Dihedral : 5.535 15.538 580 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.90 % Allowed : 13.33 % Favored : 80.77 % 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: -2.17 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 TYR 0.007 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.416 Fit side-chains REVERT: A 80 LYS cc_start: 0.7371 (tttt) cc_final: 0.6725 (pttp) REVERT: B 80 LYS cc_start: 0.7216 (tttt) cc_final: 0.6659 (pttp) REVERT: H 42 SER cc_start: 0.8899 (t) cc_final: 0.8698 (t) outliers start: 23 outliers final: 20 residues processed: 108 average time/residue: 0.1137 time to fit residues: 16.1343 Evaluate side-chains 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 3900 Z= 0.556 Angle : 0.830 5.560 5290 Z= 0.478 Chirality : 0.056 0.222 710 Planarity : 0.004 0.017 660 Dihedral : 6.526 18.226 580 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 8.97 % Allowed : 13.33 % Favored : 77.69 % 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: -2.25 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS F 50 TYR 0.020 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7466 (tttt) cc_final: 0.6878 (pttp) REVERT: B 80 LYS cc_start: 0.7220 (tttt) cc_final: 0.6925 (pttp) REVERT: C 80 LYS cc_start: 0.7001 (tttt) cc_final: 0.6757 (tttt) REVERT: E 80 LYS cc_start: 0.7171 (tttt) cc_final: 0.6379 (tptt) REVERT: F 80 LYS cc_start: 0.6950 (tttt) cc_final: 0.6125 (tptt) REVERT: G 50 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.7235 (m-70) REVERT: J 80 LYS cc_start: 0.7420 (tttt) cc_final: 0.6904 (tptt) REVERT: J 87 SER cc_start: 0.7521 (t) cc_final: 0.7284 (p) REVERT: J 88 ILE cc_start: 0.6025 (pt) cc_final: 0.5732 (pt) outliers start: 35 outliers final: 28 residues processed: 120 average time/residue: 0.1119 time to fit residues: 17.6282 Evaluate side-chains 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3900 Z= 0.329 Angle : 0.654 4.956 5290 Z= 0.383 Chirality : 0.052 0.188 710 Planarity : 0.003 0.014 660 Dihedral : 6.042 15.922 580 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 8.46 % Allowed : 16.67 % Favored : 74.87 % 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: -2.21 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 TYR 0.010 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7427 (tttt) cc_final: 0.6851 (pttp) REVERT: E 80 LYS cc_start: 0.7054 (tttt) cc_final: 0.6616 (mttm) REVERT: F 80 LYS cc_start: 0.6855 (tttt) cc_final: 0.6298 (tttt) REVERT: G 80 LYS cc_start: 0.6960 (tttt) cc_final: 0.6559 (mttt) REVERT: H 42 SER cc_start: 0.8908 (m) cc_final: 0.8661 (p) REVERT: J 80 LYS cc_start: 0.7360 (tttt) cc_final: 0.7090 (tttt) REVERT: J 88 ILE cc_start: 0.6323 (pt) cc_final: 0.5978 (pt) outliers start: 33 outliers final: 28 residues processed: 121 average time/residue: 0.1082 time to fit residues: 17.2939 Evaluate side-chains 121 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3900 Z= 0.284 Angle : 0.610 5.062 5290 Z= 0.361 Chirality : 0.051 0.180 710 Planarity : 0.002 0.012 660 Dihedral : 5.696 16.490 580 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 7.44 % Allowed : 17.95 % Favored : 74.62 % 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: -2.27 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS H 50 TYR 0.010 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7401 (tttt) cc_final: 0.6897 (pttp) REVERT: C 42 SER cc_start: 0.8720 (t) cc_final: 0.8399 (m) REVERT: D 80 LYS cc_start: 0.7047 (tttt) cc_final: 0.6815 (tttt) REVERT: E 42 SER cc_start: 0.8766 (t) cc_final: 0.8461 (p) REVERT: E 80 LYS cc_start: 0.6886 (tttt) cc_final: 0.6600 (mttt) REVERT: F 80 LYS cc_start: 0.6856 (tttt) cc_final: 0.6099 (tttt) REVERT: G 80 LYS cc_start: 0.6853 (tttt) cc_final: 0.6550 (mttt) outliers start: 29 outliers final: 26 residues processed: 118 average time/residue: 0.1032 time to fit residues: 16.1669 Evaluate side-chains 125 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 0.0980 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3900 Z= 0.294 Angle : 0.605 5.403 5290 Z= 0.357 Chirality : 0.051 0.169 710 Planarity : 0.002 0.013 660 Dihedral : 5.631 16.920 580 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 8.21 % Allowed : 19.23 % Favored : 72.56 % 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: -2.28 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 TYR 0.010 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7408 (tttt) cc_final: 0.6933 (pttp) REVERT: C 65 ASN cc_start: 0.6657 (m-40) cc_final: 0.6433 (t0) REVERT: D 80 LYS cc_start: 0.7050 (tttt) cc_final: 0.6758 (tttt) REVERT: E 42 SER cc_start: 0.8830 (t) cc_final: 0.8504 (p) REVERT: E 80 LYS cc_start: 0.6960 (tttt) cc_final: 0.6696 (mttt) REVERT: F 80 LYS cc_start: 0.7006 (tttt) cc_final: 0.6220 (tptt) REVERT: G 80 LYS cc_start: 0.6907 (tttt) cc_final: 0.6627 (mttt) outliers start: 32 outliers final: 28 residues processed: 120 average time/residue: 0.1038 time to fit residues: 16.5501 Evaluate side-chains 130 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 0.0070 chunk 45 optimal weight: 0.0770 chunk 39 optimal weight: 7.9990 overall best weight: 4.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3900 Z= 0.368 Angle : 0.659 5.477 5290 Z= 0.387 Chirality : 0.052 0.177 710 Planarity : 0.003 0.014 660 Dihedral : 5.898 18.498 580 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 7.44 % Allowed : 19.49 % Favored : 73.08 % 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: -2.31 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 TYR 0.013 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7461 (tttt) cc_final: 0.7004 (pttp) REVERT: C 65 ASN cc_start: 0.6710 (m-40) cc_final: 0.6461 (t0) REVERT: E 80 LYS cc_start: 0.6974 (tttt) cc_final: 0.6766 (mttt) REVERT: F 80 LYS cc_start: 0.7119 (tttt) cc_final: 0.6322 (tptt) REVERT: G 80 LYS cc_start: 0.6860 (tttt) cc_final: 0.6579 (mttt) outliers start: 29 outliers final: 27 residues processed: 108 average time/residue: 0.1033 time to fit residues: 14.4851 Evaluate side-chains 116 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 overall best weight: 5.8986 ------------------------------------------------------------------------------- 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: 0.6115 moved from start: 0.7261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 3900 Z= 0.516 Angle : 0.775 7.419 5290 Z= 0.445 Chirality : 0.054 0.191 710 Planarity : 0.003 0.017 660 Dihedral : 6.451 18.938 580 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 7.95 % Allowed : 20.26 % Favored : 71.79 % 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: -2.41 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 50 TYR 0.016 0.003 TYR I 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7485 (tttt) cc_final: 0.7041 (pttp) REVERT: C 65 ASN cc_start: 0.6848 (m-40) cc_final: 0.6547 (t0) REVERT: D 80 LYS cc_start: 0.7013 (tttt) cc_final: 0.6417 (mttp) REVERT: E 80 LYS cc_start: 0.7112 (tttt) cc_final: 0.6771 (mttm) REVERT: F 80 LYS cc_start: 0.7226 (tttt) cc_final: 0.6394 (tptt) REVERT: G 80 LYS cc_start: 0.6896 (tttt) cc_final: 0.6579 (mttt) REVERT: H 60 LYS cc_start: 0.4013 (mmmm) cc_final: 0.3412 (tmtt) REVERT: I 88 ILE cc_start: 0.6585 (pt) cc_final: 0.6176 (mt) REVERT: J 50 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7119 (m-70) REVERT: J 80 LYS cc_start: 0.7436 (tttt) cc_final: 0.6960 (mmtm) outliers start: 31 outliers final: 27 residues processed: 113 average time/residue: 0.1468 time to fit residues: 21.4317 Evaluate side-chains 118 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.228063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.207772 restraints weight = 5496.070| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 3.24 r_work: 0.4612 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4608 r_free = 0.4608 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4566 r_free = 0.4566 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3900 Z= 0.269 Angle : 0.610 6.170 5290 Z= 0.353 Chirality : 0.052 0.161 710 Planarity : 0.002 0.011 660 Dihedral : 5.853 26.663 580 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 7.18 % Allowed : 20.77 % Favored : 72.05 % 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: -2.38 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 TYR 0.009 0.002 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1217.14 seconds wall clock time: 26 minutes 51.31 seconds (1611.31 seconds total)