Starting phenix.real_space_refine on Thu Dec 7 19:25:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/12_2023/7ozh_13124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/12_2023/7ozh_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_13124/12_2023/7ozh_13124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/12_2023/7ozh_13124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/12_2023/7ozh_13124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/12_2023/7ozh_13124.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.47, per 1000 atoms: 0.63 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: 1.40 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.52 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: 0.95 Time building geometry restraints manager: 1.55 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 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- 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 : 0.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1311 time to fit residues: 16.5132 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5141 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5932 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3900 Z= 0.479 Angle : 0.882 6.513 5290 Z= 0.500 Chirality : 0.054 0.195 710 Planarity : 0.004 0.025 660 Dihedral : 6.833 23.224 580 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.08 % Allowed : 7.44 % Favored : 89.49 % 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 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS I 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 128 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.371 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.1548 time to fit residues: 22.9985 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0390 time to fit residues: 1.2190 ------------------------------------------------------------------------------- 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: 10.0000 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** 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: 0.5914 moved from start: 0.4810 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= 0.362 Angle : 0.719 5.708 5290 Z= 0.416 Chirality : 0.052 0.238 710 Planarity : 0.003 0.019 660 Dihedral : 6.246 19.468 580 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.33 % Allowed : 12.05 % 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: -2.16 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 50 TYR 0.012 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 115 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.417 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.1210 time to fit residues: 16.5073 Evaluate side-chains 102 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0377 time to fit residues: 1.1512 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3900 Z= 0.287 Angle : 0.633 5.267 5290 Z= 0.371 Chirality : 0.050 0.185 710 Planarity : 0.002 0.017 660 Dihedral : 5.845 17.999 580 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.08 % Allowed : 16.41 % Favored : 80.51 % 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: -2.20 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.24), 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 *********************** 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 115 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.415 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.1146 time to fit residues: 16.5046 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0416 time to fit residues: 1.2045 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** 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: 0.6074 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 3900 Z= 0.574 Angle : 0.848 5.920 5290 Z= 0.487 Chirality : 0.055 0.252 710 Planarity : 0.004 0.017 660 Dihedral : 6.820 20.342 580 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 5.38 % Allowed : 17.18 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 50 TYR 0.018 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 116 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.398 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 105 average time/residue: 0.1214 time to fit residues: 16.6574 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0355 time to fit residues: 1.5613 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3900 Z= 0.279 Angle : 0.626 5.602 5290 Z= 0.367 Chirality : 0.051 0.213 710 Planarity : 0.002 0.017 660 Dihedral : 6.030 19.897 580 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.56 % Allowed : 21.28 % Favored : 76.15 % 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: -2.43 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (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 *********************** 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 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.1236 time to fit residues: 17.5736 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0437 time to fit residues: 1.1320 ------------------------------------------------------------------------------- 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: 0.1980 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3900 Z= 0.287 Angle : 0.606 5.611 5290 Z= 0.356 Chirality : 0.051 0.189 710 Planarity : 0.002 0.016 660 Dihedral : 5.831 18.065 580 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.33 % Allowed : 21.54 % Favored : 75.13 % 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: -2.45 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 TYR 0.008 0.002 TYR F 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 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.445 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 101 average time/residue: 0.1199 time to fit residues: 15.9161 Evaluate side-chains 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0398 time to fit residues: 1.2627 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3900 Z= 0.294 Angle : 0.601 5.310 5290 Z= 0.352 Chirality : 0.051 0.186 710 Planarity : 0.002 0.016 660 Dihedral : 5.698 17.821 580 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 TYR 0.010 0.002 TYR F 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 116 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.426 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 108 average time/residue: 0.1156 time to fit residues: 16.4195 Evaluate side-chains 101 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0381 time to fit residues: 1.0213 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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: 0.6064 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 3900 Z= 0.434 Angle : 0.712 6.343 5290 Z= 0.408 Chirality : 0.052 0.144 710 Planarity : 0.003 0.017 660 Dihedral : 6.185 18.921 580 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.56 % Allowed : 22.31 % Favored : 75.13 % 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: -2.53 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 50 TYR 0.013 0.003 TYR F 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 102 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.1299 time to fit residues: 16.2550 Evaluate side-chains 95 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0393 time to fit residues: 1.1356 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 42 optimal weight: 0.0040 chunk 12 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.7798 ------------------------------------------------------------------------------- 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: 0.6068 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3900 Z= 0.426 Angle : 0.714 7.330 5290 Z= 0.406 Chirality : 0.052 0.143 710 Planarity : 0.003 0.017 660 Dihedral : 6.181 19.538 580 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.51 % Allowed : 24.62 % 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: -2.62 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 TYR 0.013 0.003 TYR F 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 90 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.448 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.1281 time to fit residues: 15.0376 Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0396 time to fit residues: 0.6806 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 0.0050 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- 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** ** 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 = 0.4917 r_free = 0.4917 target = 0.225720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.206460 restraints weight = 5723.860| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 3.36 r_work: 0.4622 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4601 r_free = 0.4601 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4565 r_free = 0.4565 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.7404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3900 Z= 0.226 Angle : 0.575 6.108 5290 Z= 0.330 Chirality : 0.050 0.134 710 Planarity : 0.002 0.016 660 Dihedral : 5.577 17.345 580 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.54 % Allowed : 24.36 % Favored : 74.10 % 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 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 TYR 0.007 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1225.84 seconds wall clock time: 22 minutes 58.89 seconds (1378.89 seconds total)