Starting phenix.real_space_refine (version: dev) on Wed Feb 22 16:41:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/02_2023/7lya_23590.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/02_2023/7lya_23590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/02_2023/7lya_23590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/02_2023/7lya_23590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/02_2023/7lya_23590.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/02_2023/7lya_23590.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12098 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 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: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 6.94, per 1000 atoms: 0.57 Number of scatterers: 12098 At special positions: 0 Unit cell: (86.604, 126.813, 117.534, 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 14 16.00 P 293 15.00 O 2829 8.00 N 2275 7.00 C 6687 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: 4.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.4% alpha, 3.1% beta 139 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.539A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.606A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.719A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.550A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.595A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.538A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.605A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.694A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.555A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.600A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.607A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.520A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.507A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.732A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.697A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.695A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.127A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.165A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.378A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 393 hydrogen bonds defined for protein. 1160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 5.26 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: 2063 1.33 - 1.45: 4276 1.45 - 1.57: 5962 1.57 - 1.68: 584 1.68 - 1.80: 24 Bond restraints: 12909 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB ARG E 131 " pdb=" CG ARG E 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG C 35 " pdb=" CG ARG C 35 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CB LEU D 80 " pdb=" CG LEU D 80 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.26e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.04: 1266 105.04 - 111.92: 7038 111.92 - 118.80: 3279 118.80 - 125.68: 6124 125.68 - 132.56: 977 Bond angle restraints: 18684 Sorted by residual: angle pdb=" C GLN A 76 " pdb=" N ASP A 77 " pdb=" CA ASP A 77 " ideal model delta sigma weight residual 122.06 114.13 7.93 1.86e+00 2.89e-01 1.82e+01 angle pdb=" C GLN E 76 " pdb=" N ASP E 77 " pdb=" CA ASP E 77 " ideal model delta sigma weight residual 122.06 114.20 7.86 1.86e+00 2.89e-01 1.79e+01 angle pdb=" C LEU B 22 " pdb=" CA LEU B 22 " pdb=" CB LEU B 22 " ideal model delta sigma weight residual 110.96 115.76 -4.80 1.54e+00 4.22e-01 9.71e+00 angle pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " ideal model delta sigma weight residual 116.92 120.09 -3.17 1.16e+00 7.43e-01 7.48e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.59 -6.41 2.37e+00 1.78e-01 7.33e+00 ... (remaining 18679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 5342 34.23 - 68.45: 1406 68.45 - 102.68: 15 102.68 - 136.91: 0 136.91 - 171.14: 2 Dihedral angle restraints: 6765 sinusoidal: 4542 harmonic: 2223 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 48.86 171.14 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 71.26 148.74 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1134 0.029 - 0.058: 688 0.058 - 0.087: 220 0.087 - 0.116: 61 0.116 - 0.144: 21 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ASP E 77 " pdb=" N ASP E 77 " pdb=" C ASP E 77 " pdb=" CB ASP E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2121 not shown) Planarity restraints: 1349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -52 " -0.007 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG I -52 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -52 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -52 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I -52 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG I -52 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DG I -52 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG I -52 " 0.030 2.00e-02 2.50e+03 pdb=" N2 DG I -52 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -52 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.53e+00 pdb=" N9 DG I 47 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " 0.024 2.00e-02 2.50e+03 1.05e-02 3.03e+00 pdb=" N9 DA I 57 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " -0.004 2.00e-02 2.50e+03 ... (remaining 1346 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1674 2.76 - 3.47: 14035 3.47 - 4.19: 34080 4.19 - 4.90: 51718 Nonbonded interactions: 101509 Sorted by model distance: nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.325 3.350 nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.173 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.209 2.440 nonbonded pdb=" O SER D 123 " pdb=" N SER C 11 " model vdw 2.239 2.520 ... (remaining 101504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 14 5.16 5 C 6687 2.51 5 N 2275 2.21 5 O 2829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 4.710 Check model and map are aligned: 0.180 Process input model: 35.430 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.007 0.046 12909 Z= 0.417 Angle : 0.671 7.927 18684 Z= 0.414 Chirality : 0.041 0.144 2124 Planarity : 0.004 0.040 1349 Dihedral : 27.513 171.135 5333 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.16 % 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: -1.91 (0.26), residues: 752 helix: -0.60 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -2.78 (0.30), residues: 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.941 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 2.1735 time to fit residues: 246.4751 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN F 27 GLN F 75 HIS H 49 HIS C 73 ASN G 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12909 Z= 0.175 Angle : 0.539 5.933 18684 Z= 0.329 Chirality : 0.033 0.126 2124 Planarity : 0.004 0.033 1349 Dihedral : 30.254 173.667 3803 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.41 % 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: 0.76 (0.29), residues: 752 helix: 1.43 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.03 (0.33), residues: 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.985 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 2.1050 time to fit residues: 203.9304 Evaluate side-chains 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.9262 time to fit residues: 5.1271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12909 Z= 0.241 Angle : 0.566 5.980 18684 Z= 0.341 Chirality : 0.035 0.129 2124 Planarity : 0.004 0.037 1349 Dihedral : 30.505 174.805 3803 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.88 % 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: 1.43 (0.30), residues: 752 helix: 1.91 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.121 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 2.0872 time to fit residues: 195.7966 Evaluate side-chains 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 1.3231 time to fit residues: 8.2392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.0030 chunk 54 optimal weight: 7.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 12909 Z= 0.212 Angle : 0.562 6.384 18684 Z= 0.340 Chirality : 0.034 0.127 2124 Planarity : 0.004 0.038 1349 Dihedral : 30.506 174.901 3803 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.25 % 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: 1.66 (0.30), residues: 752 helix: 2.07 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.61 (0.35), residues: 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.881 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 2.0061 time to fit residues: 184.1184 Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.5299 time to fit residues: 2.7545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 12909 Z= 0.196 Angle : 0.559 7.468 18684 Z= 0.338 Chirality : 0.034 0.125 2124 Planarity : 0.004 0.037 1349 Dihedral : 30.501 175.035 3803 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.94 % 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: 1.75 (0.30), residues: 752 helix: 2.13 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.882 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 1.9837 time to fit residues: 184.1080 Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.0972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.0060 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.0020 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12909 Z= 0.168 Angle : 0.550 6.967 18684 Z= 0.334 Chirality : 0.033 0.132 2124 Planarity : 0.004 0.036 1349 Dihedral : 30.490 175.099 3803 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.03 % 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: 1.94 (0.31), residues: 752 helix: 2.26 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.851 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 1.9754 time to fit residues: 185.4867 Evaluate side-chains 91 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 1.2777 time to fit residues: 6.6429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 12909 Z= 0.283 Angle : 0.583 7.866 18684 Z= 0.349 Chirality : 0.036 0.132 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.623 176.197 3803 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 1.41 % 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: 1.80 (0.30), residues: 752 helix: 2.13 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.909 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 2.1115 time to fit residues: 191.0519 Evaluate side-chains 84 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.4422 time to fit residues: 4.1764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 12909 Z= 0.205 Angle : 0.567 7.058 18684 Z= 0.342 Chirality : 0.034 0.152 2124 Planarity : 0.004 0.038 1349 Dihedral : 30.619 176.047 3803 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.41 % 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: 1.94 (0.30), residues: 752 helix: 2.22 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.902 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 2.0442 time to fit residues: 178.7971 Evaluate side-chains 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.7299 time to fit residues: 2.8589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 12909 Z= 0.289 Angle : 0.585 9.993 18684 Z= 0.349 Chirality : 0.036 0.134 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.647 176.090 3803 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.41 % 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: 1.86 (0.30), residues: 752 helix: 2.15 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.725 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 2.2546 time to fit residues: 192.0123 Evaluate side-chains 82 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.8179 time to fit residues: 4.9199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12909 Z= 0.173 Angle : 0.562 8.790 18684 Z= 0.340 Chirality : 0.034 0.158 2124 Planarity : 0.004 0.036 1349 Dihedral : 30.634 175.824 3803 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.30), residues: 752 helix: 2.36 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.952 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 2.1510 time to fit residues: 181.0631 Evaluate side-chains 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.8924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.156972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116433 restraints weight = 15576.391| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.04 r_work: 0.3160 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12909 Z= 0.215 Angle : 0.561 8.655 18684 Z= 0.338 Chirality : 0.034 0.140 2124 Planarity : 0.004 0.037 1349 Dihedral : 30.606 176.394 3803 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 752 helix: 2.33 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 209 =============================================================================== Job complete usr+sys time: 3536.08 seconds wall clock time: 63 minutes 13.15 seconds (3793.15 seconds total)