Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:03:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/11_2022/7ozh_13124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/11_2022/7ozh_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_13124/11_2022/7ozh_13124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/11_2022/7ozh_13124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/11_2022/7ozh_13124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/11_2022/7ozh_13124.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3890 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "F" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "H" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "I" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "J" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} 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: 2.28, per 1000 atoms: 0.59 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 - 3.50 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: 1.64 Conformation dependent library (CDL) restraints added in 786.2 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: 0.30 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: 0.92 Time building geometry restraints manager: 1.69 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: 104.20 - 109.50: 869 109.50 - 114.79: 1781 114.79 - 120.09: 873 120.09 - 125.39: 1757 125.39 - 130.69: 10 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 2.520 nonbonded pdb=" N VAL C 82 " pdb=" O THR E 81 " model vdw 2.546 2.520 nonbonded pdb=" N VAL E 82 " pdb=" O THR G 81 " model vdw 2.547 2.520 nonbonded pdb=" N VAL B 82 " pdb=" O THR D 81 " model vdw 2.547 2.520 nonbonded pdb=" N VAL H 82 " pdb=" O THR J 81 " model vdw 2.547 2.520 ... (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 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 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. 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: 0.710 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: 3.440 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.460 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 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 % 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 *********************** 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 : 0.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1280 time to fit residues: 16.1543 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5688 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 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** G 65 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.039 3900 Z= 0.460 Angle : 0.856 6.667 5290 Z= 0.487 Chirality : 0.053 0.196 710 Planarity : 0.004 0.023 660 Dihedral : 6.671 22.787 580 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 3.08 % 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: -1.99 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 560 *********************** 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 127 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.425 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 120 average time/residue: 0.1372 time to fit residues: 20.5740 Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.325 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0322 time to fit residues: 0.9884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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: 0.6060 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 3900 Z= 0.478 Angle : 0.812 5.721 5290 Z= 0.466 Chirality : 0.053 0.247 710 Planarity : 0.004 0.018 660 Dihedral : 6.713 19.994 580 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 3.85 % 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: -2.19 (0.32), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 560 *********************** 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 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 101 average time/residue: 0.1272 time to fit residues: 16.5830 Evaluate side-chains 102 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0388 time to fit residues: 1.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 3900 Z= 0.309 Angle : 0.660 5.162 5290 Z= 0.387 Chirality : 0.051 0.233 710 Planarity : 0.003 0.017 660 Dihedral : 6.108 19.708 580 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 3.08 % 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: -2.20 (0.32), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 560 *********************** 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 109 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.445 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.1146 time to fit residues: 15.7538 Evaluate side-chains 98 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0381 time to fit residues: 1.1657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 3900 Z= 0.433 Angle : 0.731 5.112 5290 Z= 0.426 Chirality : 0.053 0.228 710 Planarity : 0.003 0.017 660 Dihedral : 6.337 19.599 580 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 5.13 % 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: -2.35 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 560 *********************** 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 113 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.428 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 101 average time/residue: 0.1134 time to fit residues: 15.2495 Evaluate side-chains 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0391 time to fit residues: 1.7153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 3900 Z= 0.391 Angle : 0.689 5.573 5290 Z= 0.402 Chirality : 0.052 0.219 710 Planarity : 0.003 0.017 660 Dihedral : 6.252 19.734 580 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 3.85 % 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 (0.24), residues: 560 *********************** 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 109 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.1141 time to fit residues: 15.1119 Evaluate side-chains 101 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0385 time to fit residues: 1.3061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 3900 Z= 0.444 Angle : 0.723 6.503 5290 Z= 0.418 Chirality : 0.053 0.218 710 Planarity : 0.003 0.017 660 Dihedral : 6.364 19.096 580 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer Outliers : 4.62 % 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: -2.53 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.24), residues: 560 *********************** 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 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.435 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 103 average time/residue: 0.1238 time to fit residues: 16.6502 Evaluate side-chains 99 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0366 time to fit residues: 1.2736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3900 Z= 0.266 Angle : 0.613 6.303 5290 Z= 0.356 Chirality : 0.051 0.181 710 Planarity : 0.002 0.016 660 Dihedral : 5.860 18.241 580 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 1.28 % 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: -2.49 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.23), residues: 560 *********************** 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 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.427 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 0.1227 time to fit residues: 16.8716 Evaluate side-chains 100 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0410 time to fit residues: 0.7864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 3900 Z= 0.485 Angle : 0.751 6.407 5290 Z= 0.430 Chirality : 0.054 0.206 710 Planarity : 0.003 0.017 660 Dihedral : 6.375 19.081 580 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer Outliers : 2.05 % 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: -2.61 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.24), residues: 560 *********************** 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 102 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.438 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 0.1322 time to fit residues: 16.6585 Evaluate side-chains 95 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0396 time to fit residues: 0.9959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.7426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 3900 Z= 0.384 Angle : 0.680 6.405 5290 Z= 0.393 Chirality : 0.052 0.210 710 Planarity : 0.003 0.017 660 Dihedral : 6.148 19.248 580 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 2.05 % 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: -2.59 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.24), residues: 560 ********************** 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 99 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.450 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 0.1271 time to fit residues: 15.8836 Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0362 time to fit residues: 0.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.220401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.201425 restraints weight = 5687.324| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 3.38 r_work: 0.4661 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.4652 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work: 0.4642 rms_B_bonded: 3.11 restraints_weight: 0.1250 r_work: 0.4632 rms_B_bonded: 3.19 restraints_weight: 0.0625 r_work: 0.4621 rms_B_bonded: 3.32 restraints_weight: 0.0312 r_work: 0.4609 rms_B_bonded: 3.48 restraints_weight: 0.0156 r_work: 0.4597 rms_B_bonded: 3.67 restraints_weight: 0.0078 r_work: 0.4584 rms_B_bonded: 3.89 restraints_weight: 0.0039 r_work: 0.4570 rms_B_bonded: 4.14 restraints_weight: 0.0020 r_work: 0.4556 rms_B_bonded: 4.44 restraints_weight: 0.0010 r_work: 0.4540 rms_B_bonded: 4.77 restraints_weight: 0.0005 r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4861 r_free = 0.4861 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4825 r_free = 0.4825 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.7578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 3900 Z= 0.326 Angle : 0.641 6.453 5290 Z= 0.370 Chirality : 0.051 0.174 710 Planarity : 0.002 0.016 660 Dihedral : 5.861 17.872 580 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer Outliers : 0.77 % 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: -2.61 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.24), residues: 560 =============================================================================== Job complete usr+sys time: 1076.87 seconds wall clock time: 20 minutes 34.82 seconds (1234.82 seconds total)