Starting phenix.real_space_refine on Sun Dec 10 00:28:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/12_2023/8pc5_17594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/12_2023/8pc5_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_17594/12_2023/8pc5_17594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/12_2023/8pc5_17594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/12_2023/8pc5_17594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pc5_17594/12_2023/8pc5_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-1.21rc1-5172/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: 6.88, per 1000 atoms: 0.54 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: 6.83 Conformation dependent library (CDL) restraints added in 1.2 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: 7.30 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: 4.74 Time building geometry restraints manager: 6.94 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.230 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 42.100 Find NCS groups from input model: 0.490 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.500 ------------------------------------------------------------------------------- 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 : 1.047 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 153 average time/residue: 0.3790 time to fit residues: 74.3926 Evaluate side-chains 102 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1120 time to fit residues: 1.5903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: D 46 HIS E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13676 Z= 0.245 Angle : 0.579 9.863 19730 Z= 0.350 Chirality : 0.036 0.135 2229 Planarity : 0.005 0.038 1479 Dihedral : 31.052 163.123 4165 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.52 % Allowed : 11.50 % Favored : 85.97 % 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: 1.19 (0.29), residues: 831 helix: 1.70 (0.22), residues: 557 sheet: -3.22 (0.80), residues: 16 loop : -0.95 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 21 HIS 0.003 0.001 HIS D 106 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 122 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.936 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 113 average time/residue: 0.3140 time to fit residues: 47.9752 Evaluate side-chains 107 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1098 time to fit residues: 2.9846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13676 Z= 0.284 Angle : 0.582 9.132 19730 Z= 0.351 Chirality : 0.036 0.131 2229 Planarity : 0.005 0.038 1479 Dihedral : 30.730 164.879 4165 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.98 % Allowed : 14.31 % Favored : 84.71 % 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: 1.20 (0.29), residues: 831 helix: 1.71 (0.22), residues: 553 sheet: -2.05 (1.00), residues: 23 loop : -0.96 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.009 0.001 PHE E 104 TYR 0.010 0.001 TYR B 51 ARG 0.004 0.000 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 111 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.016 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 106 average time/residue: 0.3874 time to fit residues: 55.3189 Evaluate side-chains 98 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1177 time to fit residues: 1.4941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN C 73 ASN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13676 Z= 0.177 Angle : 0.532 8.180 19730 Z= 0.324 Chirality : 0.033 0.127 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.333 168.770 4165 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.12 % Allowed : 14.45 % Favored : 84.43 % 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: 1.49 (0.29), residues: 831 helix: 1.85 (0.23), residues: 560 sheet: -1.59 (1.04), residues: 24 loop : -0.74 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 82 HIS 0.004 0.001 HIS F 18 PHE 0.008 0.001 PHE H 62 TYR 0.015 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 111 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.963 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 106 average time/residue: 0.3273 time to fit residues: 46.6067 Evaluate side-chains 99 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1053 time to fit residues: 1.5766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.8406 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13676 Z= 0.171 Angle : 0.531 8.932 19730 Z= 0.323 Chirality : 0.033 0.125 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.321 171.018 4165 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.26 % Allowed : 15.43 % Favored : 83.31 % 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: 1.65 (0.29), residues: 831 helix: 1.97 (0.23), residues: 559 sheet: -1.34 (1.03), residues: 24 loop : -0.66 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.007 0.001 PHE K 44 TYR 0.017 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 111 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.067 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 0.3230 time to fit residues: 45.4430 Evaluate side-chains 100 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1237 time to fit residues: 2.3069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2956 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= 0.322 Angle : 0.588 9.143 19730 Z= 0.351 Chirality : 0.037 0.131 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.504 171.079 4165 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.98 % Allowed : 15.57 % 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: 1.36 (0.29), residues: 831 helix: 1.81 (0.22), residues: 556 sheet: -1.70 (0.92), residues: 29 loop : -0.86 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 82 HIS 0.004 0.001 HIS G 31 PHE 0.011 0.002 PHE K 44 TYR 0.015 0.001 TYR K 68 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 103 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.036 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 99 average time/residue: 0.3379 time to fit residues: 45.0870 Evaluate side-chains 94 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2157 time to fit residues: 2.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8477 moved from start: 0.3030 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= 0.205 Angle : 0.552 9.303 19730 Z= 0.334 Chirality : 0.034 0.125 2229 Planarity : 0.004 0.036 1479 Dihedral : 30.399 171.346 4165 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.56 % Allowed : 15.71 % Favored : 83.73 % 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: 1.56 (0.29), residues: 831 helix: 1.89 (0.22), residues: 557 sheet: -1.22 (1.06), residues: 24 loop : -0.68 (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 F 18 PHE 0.009 0.001 PHE K 12 TYR 0.019 0.001 TYR K 68 ARG 0.004 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 99 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.3412 time to fit residues: 43.9724 Evaluate side-chains 96 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1090 time to fit residues: 1.6248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13676 Z= 0.335 Angle : 0.596 9.137 19730 Z= 0.355 Chirality : 0.037 0.131 2229 Planarity : 0.005 0.035 1479 Dihedral : 30.481 170.968 4165 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.28 % Allowed : 16.69 % Favored : 83.03 % 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: 1.40 (0.29), residues: 831 helix: 1.81 (0.22), residues: 553 sheet: -1.18 (1.05), residues: 24 loop : -0.81 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 82 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.002 PHE H 62 TYR 0.016 0.001 TYR K 68 ARG 0.005 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 95 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.3285 time to fit residues: 41.4035 Evaluate side-chains 90 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.3184 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= 0.204 Angle : 0.565 9.744 19730 Z= 0.341 Chirality : 0.035 0.128 2229 Planarity : 0.004 0.036 1479 Dihedral : 30.441 171.372 4165 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.70 % Allowed : 16.55 % 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: 1.50 (0.29), residues: 831 helix: 1.88 (0.22), residues: 553 sheet: -1.12 (1.06), residues: 24 loop : -0.75 (0.35), residues: 254 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 0.008 0.001 PHE K 44 TYR 0.019 0.001 TYR K 68 ARG 0.002 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 97 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.3377 time to fit residues: 42.7549 Evaluate side-chains 92 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1121 time to fit residues: 1.9073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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: 0.8468 moved from start: 0.3313 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= 0.200 Angle : 0.547 9.565 19730 Z= 0.330 Chirality : 0.034 0.130 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.248 172.136 4165 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 16.97 % Favored : 83.03 % 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: 1.64 (0.29), residues: 831 helix: 1.93 (0.22), residues: 558 sheet: -1.00 (1.06), residues: 24 loop : -0.64 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 82 HIS 0.004 0.001 HIS K 48 PHE 0.008 0.001 PHE H 62 TYR 0.016 0.001 TYR K 68 ARG 0.002 0.000 ARG A 129 ********************** 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 93 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.975 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3857 time to fit residues: 48.6696 Evaluate side-chains 91 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053710 restraints weight = 37848.976| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.75 r_work: 0.2713 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.3334 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= 0.211 Angle : 0.549 9.875 19730 Z= 0.331 Chirality : 0.034 0.128 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.238 172.236 4165 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.28 % Allowed : 17.39 % 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: 1.64 (0.29), residues: 831 helix: 1.93 (0.22), residues: 557 sheet: -1.00 (1.05), residues: 24 loop : -0.61 (0.36), residues: 250 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 0.008 0.001 PHE H 62 TYR 0.018 0.001 TYR K 68 ARG 0.002 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2687.66 seconds wall clock time: 49 minutes 12.21 seconds (2952.21 seconds total)