Starting phenix.real_space_refine on Fri Mar 15 21:15:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/03_2024/8pc5_17594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/03_2024/8pc5_17594.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/8pc5_17594/03_2024/8pc5_17594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/03_2024/8pc5_17594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/03_2024/8pc5_17594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/03_2024/8pc5_17594_updated.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= 0.001 sd= 0.014 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 13 5.16 5 C 7172 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 6.32, per 1000 atoms: 0.49 Number of scatterers: 12836 At special positions: 0 Unit cell: (102.533, 125.04, 123.373, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7172 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: 5.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 1 sheets defined 57.6% alpha, 2.2% beta 146 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 7.00 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.956A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.751A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.702A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 21 No H-bonds generated for 'chain 'C' and resid 18 through 21' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.373A pdb=" N VAL D 108 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.535A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.091A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 68 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.113A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing sheet with id= A, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.602A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 6.18 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: 2069 1.33 - 1.45: 4662 1.45 - 1.57: 6333 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13676 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.758 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" P DT J -72 " pdb=" OP1 DT J -72 " ideal model delta sigma weight residual 1.480 1.522 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" P DC I 69 " pdb=" OP2 DC I 69 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" P DG J 62 " pdb=" OP1 DG J 62 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.51e+00 ... (remaining 13671 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.45: 677 103.45 - 111.08: 6667 111.08 - 118.71: 4843 118.71 - 126.34: 6635 126.34 - 133.96: 908 Bond angle restraints: 19730 Sorted by residual: angle pdb=" O3' DC I 49 " pdb=" P DA I 50 " pdb=" O5' DA I 50 " ideal model delta sigma weight residual 104.00 95.83 8.17 1.50e+00 4.44e-01 2.97e+01 angle pdb=" C4' DC I 49 " pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 110.00 102.83 7.17 1.50e+00 4.44e-01 2.29e+01 angle pdb=" O3' DA J -73 " pdb=" P DT J -72 " pdb=" O5' DT J -72 " ideal model delta sigma weight residual 104.00 109.54 -5.54 1.50e+00 4.44e-01 1.36e+01 angle pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sigma weight residual 120.20 125.37 -5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sigma weight residual 120.20 125.25 -5.05 1.50e+00 4.44e-01 1.13e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 5857 35.94 - 71.87: 1586 71.87 - 107.81: 28 107.81 - 143.75: 3 143.75 - 179.69: 3 Dihedral angle restraints: 7477 sinusoidal: 5003 harmonic: 2474 Sorted by residual: dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual -140.00 39.69 -179.69 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 25.29 -165.29 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -73 " pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sinusoidal sigma weight residual -140.00 18.69 -158.69 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2146 0.113 - 0.226: 73 0.226 - 0.340: 0 0.340 - 0.453: 1 0.453 - 0.566: 9 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DA J 65 " pdb=" OP1 DA J 65 " pdb=" OP2 DA J 65 " pdb=" O5' DA J 65 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" P DT J 69 " pdb=" OP1 DT J 69 " pdb=" OP2 DT J 69 " pdb=" O5' DT J 69 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" P DG J 64 " pdb=" OP1 DG J 64 " pdb=" OP2 DG J 64 " pdb=" O5' DG J 64 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 2226 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ML3 A 36 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ML3 A 36 " -0.049 2.00e-02 2.50e+03 pdb=" O ML3 A 36 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 37 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " -0.029 2.00e-02 2.50e+03 1.85e-02 7.74e+00 pdb=" N1 DC I 49 " 0.043 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.032 2.00e-02 2.50e+03 1.56e-02 7.29e+00 pdb=" N9 DG I 47 " 0.042 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1388 2.74 - 3.28: 10800 3.28 - 3.82: 25054 3.82 - 4.36: 30356 4.36 - 4.90: 43327 Nonbonded interactions: 110925 Sorted by model distance: nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 89 " model vdw 2.205 2.520 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.218 2.440 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.259 2.520 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.263 2.520 nonbonded pdb=" O PRO K 60 " pdb=" ND2 ASN K 64 " model vdw 2.277 2.520 ... (remaining 110920 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.020 Extract box with map and model: 15.050 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 38.920 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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: 60.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 0.057 13676 Z= 0.343 Angle : 0.786 8.330 19730 Z= 0.459 Chirality : 0.060 0.566 2229 Planarity : 0.006 0.048 1479 Dihedral : 29.262 179.686 5879 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.42 % Allowed : 11.08 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 831 helix: 1.76 (0.22), residues: 541 sheet: -3.81 (0.82), residues: 12 loop : -1.27 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 21 HIS 0.006 0.002 HIS G 31 PHE 0.014 0.002 PHE A 78 TYR 0.010 0.002 TYR H 34 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8922 (m) cc_final: 0.8721 (t) outliers start: 3 outliers final: 2 residues processed: 153 average time/residue: 0.3786 time to fit residues: 74.4815 Evaluate side-chains 103 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN D 46 HIS E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.242 Angle : 0.578 9.563 19730 Z= 0.351 Chirality : 0.036 0.151 2229 Planarity : 0.005 0.038 1479 Dihedral : 30.956 162.663 4168 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.66 % Allowed : 11.92 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 831 helix: 1.68 (0.22), residues: 559 sheet: -2.36 (0.93), residues: 23 loop : -0.89 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 21 HIS 0.003 0.001 HIS K 48 PHE 0.008 0.001 PHE H 62 TYR 0.008 0.001 TYR D 37 ARG 0.004 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 SER cc_start: 0.8991 (m) cc_final: 0.8555 (t) outliers start: 19 outliers final: 8 residues processed: 115 average time/residue: 0.3036 time to fit residues: 47.4687 Evaluate side-chains 105 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13676 Z= 0.405 Angle : 0.629 9.687 19730 Z= 0.374 Chirality : 0.040 0.135 2229 Planarity : 0.005 0.038 1479 Dihedral : 30.928 167.976 4167 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.24 % Allowed : 14.31 % Favored : 83.45 % 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: 0.98 (0.28), residues: 831 helix: 1.55 (0.22), residues: 551 sheet: -2.18 (0.96), residues: 23 loop : -1.02 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.004 0.001 HIS G 31 PHE 0.010 0.002 PHE E 104 TYR 0.010 0.002 TYR B 51 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: E 79 LYS cc_start: 0.8742 (tttt) cc_final: 0.8499 (tttt) REVERT: H 84 SER cc_start: 0.9016 (m) cc_final: 0.8641 (t) outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.3252 time to fit residues: 48.5665 Evaluate side-chains 104 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13676 Z= 0.194 Angle : 0.548 8.612 19730 Z= 0.333 Chirality : 0.034 0.129 2229 Planarity : 0.004 0.040 1479 Dihedral : 30.423 162.663 4167 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.68 % Allowed : 15.43 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.29), residues: 831 helix: 1.74 (0.22), residues: 558 sheet: -1.32 (1.29), residues: 18 loop : -0.83 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 82 HIS 0.004 0.001 HIS F 18 PHE 0.006 0.001 PHE H 62 TYR 0.009 0.001 TYR K 68 ARG 0.004 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: E 79 LYS cc_start: 0.8692 (tttt) cc_final: 0.8479 (tttt) REVERT: H 84 SER cc_start: 0.8935 (m) cc_final: 0.8579 (t) REVERT: K 78 ASN cc_start: 0.6538 (p0) cc_final: 0.6305 (p0) outliers start: 12 outliers final: 7 residues processed: 111 average time/residue: 0.3064 time to fit residues: 45.9132 Evaluate side-chains 105 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 94 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13676 Z= 0.178 Angle : 0.535 8.329 19730 Z= 0.326 Chirality : 0.033 0.125 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.317 167.123 4165 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.40 % Allowed : 15.99 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 831 helix: 1.92 (0.23), residues: 559 sheet: -1.33 (1.03), residues: 24 loop : -0.70 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.010 0.001 PHE K 44 TYR 0.008 0.001 TYR K 68 ARG 0.003 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: E 79 LYS cc_start: 0.8691 (tttt) cc_final: 0.8459 (tttt) REVERT: H 84 SER cc_start: 0.8948 (m) cc_final: 0.8742 (t) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.3081 time to fit residues: 44.6900 Evaluate side-chains 107 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13676 Z= 0.267 Angle : 0.570 9.035 19730 Z= 0.342 Chirality : 0.036 0.127 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.437 171.076 4165 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.82 % Allowed : 15.85 % Favored : 82.33 % 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: 1.47 (0.29), residues: 831 helix: 1.85 (0.22), residues: 553 sheet: -1.23 (1.06), residues: 24 loop : -0.76 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.009 0.001 PHE H 62 TYR 0.010 0.001 TYR B 51 ARG 0.005 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: E 79 LYS cc_start: 0.8724 (tttt) cc_final: 0.8520 (tttt) REVERT: H 84 SER cc_start: 0.8958 (m) cc_final: 0.8699 (t) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.3212 time to fit residues: 46.5333 Evaluate side-chains 101 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.237 Angle : 0.552 9.286 19730 Z= 0.333 Chirality : 0.034 0.126 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.269 171.655 4165 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.54 % Allowed : 15.99 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.29), residues: 831 helix: 1.88 (0.22), residues: 557 sheet: -1.08 (1.04), residues: 24 loop : -0.72 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.011 0.001 PHE K 44 TYR 0.007 0.001 TYR K 68 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8948 (m) cc_final: 0.8705 (t) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.2934 time to fit residues: 41.6655 Evaluate side-chains 101 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13676 Z= 0.282 Angle : 0.571 9.663 19730 Z= 0.342 Chirality : 0.035 0.127 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.369 171.767 4165 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 15.43 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 831 helix: 1.84 (0.22), residues: 555 sheet: -1.04 (1.04), residues: 24 loop : -0.66 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE K 44 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8987 (m) cc_final: 0.8718 (t) REVERT: K 78 ASN cc_start: 0.6278 (p0) cc_final: 0.6006 (p0) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 0.3134 time to fit residues: 42.6503 Evaluate side-chains 104 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13676 Z= 0.267 Angle : 0.564 9.613 19730 Z= 0.338 Chirality : 0.035 0.124 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.276 172.165 4165 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.96 % Allowed : 15.43 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 831 helix: 1.85 (0.22), residues: 556 sheet: -0.86 (1.07), residues: 24 loop : -0.70 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 82 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE H 62 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8967 (m) cc_final: 0.8732 (t) REVERT: K 78 ASN cc_start: 0.6302 (p0) cc_final: 0.5997 (p0) outliers start: 14 outliers final: 12 residues processed: 105 average time/residue: 0.3057 time to fit residues: 43.5218 Evaluate side-chains 108 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.198 Angle : 0.560 9.738 19730 Z= 0.336 Chirality : 0.034 0.129 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.292 172.442 4165 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.54 % Allowed : 15.71 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 831 helix: 1.90 (0.23), residues: 556 sheet: -0.84 (1.08), residues: 24 loop : -0.66 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.009 0.001 PHE H 62 TYR 0.008 0.001 TYR B 51 ARG 0.002 0.000 ARG H 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8951 (m) cc_final: 0.8691 (t) REVERT: K 78 ASN cc_start: 0.6271 (p0) cc_final: 0.5965 (p0) outliers start: 11 outliers final: 11 residues processed: 103 average time/residue: 0.3153 time to fit residues: 44.0040 Evaluate side-chains 107 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053616 restraints weight = 37777.665| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.75 r_work: 0.2713 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.206 Angle : 0.554 9.975 19730 Z= 0.333 Chirality : 0.034 0.126 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.259 172.543 4165 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.26 % Allowed : 16.13 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.29), residues: 831 helix: 1.92 (0.23), residues: 556 sheet: -0.82 (1.09), residues: 24 loop : -0.63 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.009 0.001 PHE H 62 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2642.31 seconds wall clock time: 47 minutes 54.78 seconds (2874.78 seconds total)