Starting phenix.real_space_refine on Thu Nov 16 14:18:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/11_2023/7pf6_13369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/11_2023/7pf6_13369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/11_2023/7pf6_13369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/11_2023/7pf6_13369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/11_2023/7pf6_13369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/11_2023/7pf6_13369.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 7.20, per 1000 atoms: 0.53 Number of scatterers: 13470 At special positions: 0 Unit cell: (118.65, 149.1, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 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: 8.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 69.9% alpha, 2.8% beta 167 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 6.98 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.681A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.815A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.759A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.144A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.621A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.514A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.619A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.834A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 101 removed outlier: 3.513A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.856A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.835A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 75 through 90 removed outlier: 3.884A pdb=" N GLY U 90 " --> pdb=" O LEU U 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.789A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.492A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.023A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.367A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94 431 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 852 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 8.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2463 1.33 - 1.45: 4932 1.45 - 1.57: 6305 1.57 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 610 " pdb=" O3' DG J 610 " ideal model delta sigma weight residual 1.422 1.524 -0.102 3.00e-02 1.11e+03 1.15e+01 bond pdb=" C3' DT I 167 " pdb=" O3' DT I 167 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C3' DG J 675 " pdb=" O3' DG J 675 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" C ASN C 110 " pdb=" N ILE C 111 " ideal model delta sigma weight residual 1.331 1.307 0.023 1.27e-02 6.20e+03 3.40e+00 bond pdb=" CG1 ILE E 130 " pdb=" CD1 ILE E 130 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.09e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 78.27 - 90.90: 2 90.90 - 103.53: 888 103.53 - 116.16: 10421 116.16 - 128.80: 9296 128.80 - 141.43: 246 Bond angle restraints: 20853 Sorted by residual: angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 108.00 78.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP1 DG J 611 " ideal model delta sigma weight residual 108.00 85.49 22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" OP1 DG J 611 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 120.00 141.43 -21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb=" N ILE G 79 " pdb=" CA ILE G 79 " pdb=" C ILE G 79 " ideal model delta sigma weight residual 108.45 102.43 6.02 1.20e+00 6.94e-01 2.52e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 119.47 -8.45 1.86e+00 2.89e-01 2.07e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 5787 34.71 - 69.42: 1670 69.42 - 104.13: 44 104.13 - 138.84: 3 138.84 - 173.55: 3 Dihedral angle restraints: 7507 sinusoidal: 5076 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLN G 24 " pdb=" C GLN G 24 " pdb=" N PHE G 25 " pdb=" CA PHE G 25 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ILE H 54 " pdb=" C ILE H 54 " pdb=" N SER H 55 " pdb=" CA SER H 55 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2375 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.535: 0 1.535 - 1.919: 1 Chirality restraints: 2376 Sorted by residual: chirality pdb=" P DG J 611 " pdb=" OP1 DG J 611 " pdb=" OP2 DG J 611 " pdb=" O5' DG J 611 " both_signs ideal model delta sigma weight residual True 2.35 0.43 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO G 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 30 " 0.034 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC I 30 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DC I 30 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 30 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 30 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 30 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC I 30 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 30 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 30 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 103 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.035 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2943 2.79 - 3.32: 12785 3.32 - 3.85: 29386 3.85 - 4.37: 32078 4.37 - 4.90: 44329 Nonbonded interactions: 121521 Sorted by model distance: nonbonded pdb=" NZ LYS A 37 " pdb=" OP1 DC J 726 " model vdw 2.268 2.520 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.291 2.440 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.309 2.440 nonbonded pdb=" O GLU F 74 " pdb=" NH2 ARG H 92 " model vdw 2.313 2.520 nonbonded pdb=" OG SER F 47 " pdb=" OP1 DC J 662 " model vdw 2.314 2.440 ... (remaining 121516 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.140 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 46.670 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.006 0.102 14386 Z= 0.360 Angle : 0.986 29.733 20853 Z= 0.539 Chirality : 0.064 1.919 2376 Planarity : 0.008 0.084 1478 Dihedral : 29.659 173.553 5941 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.75 (0.26), residues: 825 helix: -0.26 (0.20), residues: 573 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2628 time to fit residues: 65.4317 Evaluate side-chains 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14386 Z= 0.275 Angle : 0.750 28.414 20853 Z= 0.421 Chirality : 0.054 1.904 2376 Planarity : 0.005 0.059 1478 Dihedral : 33.212 170.499 4289 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.02 % Allowed : 11.40 % Favored : 86.58 % 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: 0.60 (0.28), residues: 825 helix: 0.84 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -0.46 (0.35), residues: 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 0.2408 time to fit residues: 50.7689 Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1596 time to fit residues: 3.8869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 84 ASN G 73 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 14386 Z= 0.427 Angle : 0.846 30.013 20853 Z= 0.473 Chirality : 0.057 1.856 2376 Planarity : 0.007 0.061 1478 Dihedral : 33.740 172.246 4289 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.88 % Allowed : 16.45 % Favored : 81.67 % 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: 0.09 (0.27), residues: 825 helix: 0.41 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.57 (0.36), residues: 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 128 average time/residue: 0.2513 time to fit residues: 47.3591 Evaluate side-chains 114 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1166 time to fit residues: 2.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14386 Z= 0.257 Angle : 0.738 27.999 20853 Z= 0.415 Chirality : 0.055 1.927 2376 Planarity : 0.005 0.044 1478 Dihedral : 33.503 173.280 4289 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.59 % Allowed : 19.05 % Favored : 79.37 % 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: 0.64 (0.28), residues: 825 helix: 0.85 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 134 average time/residue: 0.2732 time to fit residues: 53.7830 Evaluate side-chains 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1321 time to fit residues: 2.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14386 Z= 0.284 Angle : 0.754 28.103 20853 Z= 0.422 Chirality : 0.056 1.945 2376 Planarity : 0.005 0.046 1478 Dihedral : 33.501 171.358 4289 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.59 % Allowed : 21.79 % Favored : 76.62 % 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: 0.62 (0.28), residues: 825 helix: 0.86 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.55 (0.36), residues: 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 129 average time/residue: 0.2576 time to fit residues: 48.4748 Evaluate side-chains 116 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1172 time to fit residues: 2.3913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14386 Z= 0.240 Angle : 0.738 27.403 20853 Z= 0.411 Chirality : 0.055 1.969 2376 Planarity : 0.004 0.045 1478 Dihedral : 33.409 171.957 4289 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.01 % Allowed : 22.66 % Favored : 76.33 % 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: 0.77 (0.28), residues: 825 helix: 1.02 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 127 average time/residue: 0.2762 time to fit residues: 51.8817 Evaluate side-chains 122 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1394 time to fit residues: 2.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14386 Z= 0.239 Angle : 0.730 27.210 20853 Z= 0.408 Chirality : 0.055 1.987 2376 Planarity : 0.004 0.054 1478 Dihedral : 33.294 170.799 4289 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.87 % Allowed : 24.10 % Favored : 75.04 % 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: 0.74 (0.28), residues: 825 helix: 1.03 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 128 average time/residue: 0.2757 time to fit residues: 50.5498 Evaluate side-chains 119 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1169 time to fit residues: 1.7222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 14386 Z= 0.361 Angle : 0.802 28.569 20853 Z= 0.448 Chirality : 0.057 1.941 2376 Planarity : 0.006 0.051 1478 Dihedral : 33.674 171.748 4289 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 24.96 % Favored : 73.74 % 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: 0.25 (0.28), residues: 825 helix: 0.67 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.88 (0.34), residues: 245 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 128 average time/residue: 0.2689 time to fit residues: 50.3777 Evaluate side-chains 123 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1276 time to fit residues: 2.5875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14386 Z= 0.322 Angle : 0.802 27.745 20853 Z= 0.445 Chirality : 0.057 1.982 2376 Planarity : 0.005 0.046 1478 Dihedral : 33.685 172.402 4289 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 27.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.15 % Allowed : 25.83 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 825 helix: 0.61 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.85 (0.35), residues: 245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 0.2606 time to fit residues: 46.7408 Evaluate side-chains 121 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1123 time to fit residues: 2.1535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14386 Z= 0.317 Angle : 0.812 27.799 20853 Z= 0.450 Chirality : 0.058 1.979 2376 Planarity : 0.005 0.047 1478 Dihedral : 33.733 171.420 4289 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 27.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.43 % Allowed : 26.70 % Favored : 72.87 % 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: 0.08 (0.28), residues: 825 helix: 0.54 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 245 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 120 average time/residue: 0.2648 time to fit residues: 46.6332 Evaluate side-chains 118 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1215 time to fit residues: 1.9156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3633 r_free = 0.3633 target = 0.049074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.040688 restraints weight = 131132.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.041710 restraints weight = 78759.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.042386 restraints weight = 55734.608| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14386 Z= 0.285 Angle : 0.800 27.039 20853 Z= 0.442 Chirality : 0.058 2.032 2376 Planarity : 0.005 0.047 1478 Dihedral : 33.653 171.559 4289 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.14 % Allowed : 27.13 % Favored : 72.73 % 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: 0.11 (0.28), residues: 825 helix: 0.57 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.95 (0.35), residues: 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.25 seconds wall clock time: 39 minutes 53.96 seconds (2393.96 seconds total)