Starting phenix.real_space_refine on Fri Mar 15 23:38:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/03_2024/8t9f_41109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/03_2024/8t9f_41109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/03_2024/8t9f_41109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/03_2024/8t9f_41109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/03_2024/8t9f_41109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/03_2024/8t9f_41109_updated.pdb" } resolution = 2.6 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= 0.005 sd= 0.041 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 244 5.49 5 S 30 5.16 5 C 7475 2.51 5 N 2445 2.21 5 O 2938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13132 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2060 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2484 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2518 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 698 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 781 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 835 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 7.48, per 1000 atoms: 0.57 Number of scatterers: 13132 At special positions: 0 Unit cell: (97.11, 117.611, 118.69, 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 30 16.00 P 244 15.00 O 2938 8.00 N 2445 7.00 C 7475 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: 6.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 3 sheets defined 56.6% alpha, 2.7% beta 122 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'K' and resid 74 through 87 Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 134 through 147 Processing helix chain 'K' and resid 150 through 159 removed outlier: 3.646A pdb=" N SER K 159 " --> pdb=" O LYS K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 168 Processing helix chain 'K' and resid 172 through 189 removed outlier: 3.779A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE K 189 " --> pdb=" O TYR K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 241 Processing helix chain 'K' and resid 267 through 270 removed outlier: 3.679A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 267 through 270' Processing helix chain 'K' and resid 322 through 327 Processing helix chain 'K' and resid 330 through 332 No H-bonds generated for 'chain 'K' and resid 330 through 332' Processing helix chain 'K' and resid 355 through 361 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.635A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.758A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 19 through 22 No H-bonds generated for 'chain 'G' and resid 19 through 22' Processing helix chain 'G' and resid 29 through 38 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.663A pdb=" N THR H 123 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.032A 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 130 Processing helix chain 'C' and resid 19 through 22 No H-bonds generated for 'chain 'C' and resid 19 through 22' Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 48 through 75 Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 115 through 118 No H-bonds generated for 'chain 'C' and resid 115 through 118' Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.511A pdb=" N THR D 122 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 195 through 199 Processing sheet with id= B, first strand: chain 'K' and resid 230 through 234 removed outlier: 4.344A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 279 through 283 412 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2736 1.33 - 1.45: 4080 1.45 - 1.57: 6509 1.57 - 1.69: 486 1.69 - 1.81: 47 Bond restraints: 13858 Sorted by residual: bond pdb=" N GLN K 374 " pdb=" CA GLN K 374 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.38e+00 bond pdb=" C2 SAM K 401 " pdb=" N3 SAM K 401 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" N ASP K 372 " pdb=" CA ASP K 372 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.42e+00 bond pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " ideal model delta sigma weight residual 1.422 1.503 -0.081 3.00e-02 1.11e+03 7.33e+00 bond pdb=" C8 SAM K 401 " pdb=" N7 SAM K 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.05e+00 ... (remaining 13853 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.06: 1074 105.06 - 112.27: 7633 112.27 - 119.49: 4257 119.49 - 126.70: 6030 126.70 - 133.91: 744 Bond angle restraints: 19738 Sorted by residual: angle pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sigma weight residual 120.20 125.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" N ASP K 372 " pdb=" CA ASP K 372 " pdb=" C ASP K 372 " ideal model delta sigma weight residual 112.57 108.70 3.87 1.13e+00 7.83e-01 1.17e+01 angle pdb=" CA ASN K 370 " pdb=" C ASN K 370 " pdb=" O ASN K 370 " ideal model delta sigma weight residual 121.99 118.36 3.63 1.14e+00 7.69e-01 1.01e+01 angle pdb=" O4' DT J 28 " pdb=" C1' DT J 28 " pdb=" N1 DT J 28 " ideal model delta sigma weight residual 108.40 113.13 -4.73 1.50e+00 4.44e-01 9.96e+00 angle pdb=" CA SER K 371 " pdb=" C SER K 371 " pdb=" O SER K 371 " ideal model delta sigma weight residual 121.56 118.19 3.37 1.09e+00 8.42e-01 9.55e+00 ... (remaining 19733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 6504 35.14 - 70.28: 1200 70.28 - 105.42: 18 105.42 - 140.57: 1 140.57 - 175.71: 3 Dihedral angle restraints: 7726 sinusoidal: 4741 harmonic: 2985 Sorted by residual: dihedral pdb=" C4' DA J 110 " pdb=" C3' DA J 110 " pdb=" O3' DA J 110 " pdb=" P DC J 111 " ideal model delta sinusoidal sigma weight residual -140.00 35.71 -175.71 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 106 " pdb=" C3' DG J 106 " pdb=" O3' DG J 106 " pdb=" P DT J 107 " ideal model delta sinusoidal sigma weight residual 220.00 47.47 172.53 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 27 " pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sinusoidal sigma weight residual -140.00 15.85 -155.85 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1742 0.042 - 0.084: 398 0.084 - 0.126: 90 0.126 - 0.167: 4 0.167 - 0.209: 2 Chirality restraints: 2236 Sorted by residual: chirality pdb=" P DT J 28 " pdb=" OP1 DT J 28 " pdb=" OP2 DT J 28 " pdb=" O5' DT J 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2' SAM K 401 " pdb=" C1' SAM K 401 " pdb=" C3' SAM K 401 " pdb=" O2' SAM K 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.56 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" C1' SAM K 401 " pdb=" C2' SAM K 401 " pdb=" N9 SAM K 401 " pdb=" O4' SAM K 401 " both_signs ideal model delta sigma weight residual False 2.30 2.46 -0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2233 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 27 " 0.050 2.00e-02 2.50e+03 2.91e-02 1.91e+01 pdb=" N1 DC J 27 " -0.039 2.00e-02 2.50e+03 pdb=" C2 DC J 27 " -0.034 2.00e-02 2.50e+03 pdb=" O2 DC J 27 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC J 27 " 0.031 2.00e-02 2.50e+03 pdb=" C4 DC J 27 " -0.024 2.00e-02 2.50e+03 pdb=" N4 DC J 27 " 0.030 2.00e-02 2.50e+03 pdb=" C5 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 27 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C GLU B 63 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LYS B 59 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS B 59 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 60 " 0.012 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 5 2.16 - 2.84: 3798 2.84 - 3.53: 17635 3.53 - 4.21: 34895 4.21 - 4.90: 53635 Nonbonded interactions: 109968 Sorted by model distance: nonbonded pdb=" OH TYR K 306 " pdb=" OD1 ASP K 309 " model vdw 1.469 2.440 nonbonded pdb=" CD2 LEU K 150 " pdb=" CE1 PHE K 183 " model vdw 1.636 3.760 nonbonded pdb=" O GLU K 325 " pdb=" CE2 PHE K 332 " model vdw 2.081 3.340 nonbonded pdb=" CD2 LEU K 150 " pdb=" CD1 PHE K 183 " model vdw 2.084 3.760 nonbonded pdb=" CD2 LEU K 150 " pdb=" CZ PHE K 183 " model vdw 2.106 3.760 ... (remaining 109963 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' and resid 40 through 135) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.050 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: 7.440 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 43.940 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.004 0.081 13858 Z= 0.216 Angle : 0.589 8.743 19738 Z= 0.351 Chirality : 0.037 0.209 2236 Planarity : 0.004 0.049 1658 Dihedral : 25.251 175.707 5798 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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: 1.11 (0.25), residues: 1009 helix: 1.75 (0.20), residues: 635 sheet: 0.01 (0.71), residues: 44 loop : -1.20 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 66 TYR 0.009 0.001 TYR E 54 ARG 0.002 0.000 ARG K 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8728 (mm-30) REVERT: K 225 GLU cc_start: 0.7675 (pt0) cc_final: 0.7339 (tp30) REVERT: A 81 ASP cc_start: 0.8311 (m-30) cc_final: 0.8081 (m-30) REVERT: F 44 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8473 (mtpp) REVERT: D 42 TYR cc_start: 0.8146 (t80) cc_final: 0.7929 (t80) outliers start: 0 outliers final: 1 residues processed: 225 average time/residue: 1.6374 time to fit residues: 392.9073 Evaluate side-chains 166 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 271 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 GLN K 207 GLN K 273 HIS ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 25 ASN A 85 GLN F 25 ASN G 26 GLN E 68 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13858 Z= 0.266 Angle : 0.541 8.368 19738 Z= 0.324 Chirality : 0.036 0.147 2236 Planarity : 0.005 0.041 1658 Dihedral : 29.618 179.635 3830 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.67 % Allowed : 13.86 % Favored : 82.46 % 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: 1.32 (0.26), residues: 1009 helix: 1.95 (0.21), residues: 637 sheet: -0.03 (0.72), residues: 44 loop : -1.17 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.009 0.001 PHE K 281 TYR 0.013 0.001 TYR E 54 ARG 0.007 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: K 187 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8705 (tpp80) REVERT: K 225 GLU cc_start: 0.7808 (pt0) cc_final: 0.7400 (tp30) REVERT: G 25 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8905 (pp) REVERT: G 74 LYS cc_start: 0.8160 (tptt) cc_final: 0.7936 (mmmt) outliers start: 31 outliers final: 14 residues processed: 186 average time/residue: 1.6427 time to fit residues: 326.1725 Evaluate side-chains 174 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8499 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13858 Z= 0.234 Angle : 0.520 6.700 19738 Z= 0.313 Chirality : 0.035 0.131 2236 Planarity : 0.004 0.039 1658 Dihedral : 29.564 177.271 3828 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.84 % Allowed : 16.47 % Favored : 80.69 % 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 (0.27), residues: 1009 helix: 1.98 (0.21), residues: 636 sheet: -0.11 (0.72), residues: 44 loop : -1.14 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.008 0.001 PHE K 281 TYR 0.010 0.001 TYR D 40 ARG 0.007 0.001 ARG K 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: K 187 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8723 (tpp80) REVERT: K 225 GLU cc_start: 0.7895 (pt0) cc_final: 0.7413 (tp30) REVERT: A 133 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: G 74 LYS cc_start: 0.8110 (tptt) cc_final: 0.7899 (mmmt) outliers start: 24 outliers final: 18 residues processed: 181 average time/residue: 1.6175 time to fit residues: 313.1219 Evaluate side-chains 182 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 278 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.214 Angle : 0.510 6.604 19738 Z= 0.307 Chirality : 0.034 0.129 2236 Planarity : 0.004 0.038 1658 Dihedral : 29.463 177.598 3828 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.03 % Allowed : 15.40 % Favored : 80.57 % 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: 1.44 (0.27), residues: 1009 helix: 2.01 (0.21), residues: 639 sheet: -0.05 (0.78), residues: 38 loop : -1.06 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.003 0.000 HIS H 83 PHE 0.007 0.001 PHE K 281 TYR 0.010 0.001 TYR D 40 ARG 0.009 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.7891 (pt0) cc_final: 0.7393 (tp30) REVERT: A 133 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: F 44 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8452 (mtpt) REVERT: G 25 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8980 (pp) REVERT: G 67 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: G 74 LYS cc_start: 0.8107 (tptt) cc_final: 0.7899 (mmmt) REVERT: C 67 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7915 (tp30) outliers start: 34 outliers final: 18 residues processed: 188 average time/residue: 1.6089 time to fit residues: 323.2911 Evaluate side-chains 184 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0020 chunk 1 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13858 Z= 0.351 Angle : 0.563 6.994 19738 Z= 0.335 Chirality : 0.038 0.136 2236 Planarity : 0.005 0.038 1658 Dihedral : 29.665 179.651 3828 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.15 % Allowed : 15.64 % Favored : 80.21 % 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 (0.27), residues: 1009 helix: 1.82 (0.21), residues: 637 sheet: -0.15 (0.77), residues: 38 loop : -1.11 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 264 HIS 0.004 0.001 HIS G 43 PHE 0.010 0.001 PHE K 281 TYR 0.023 0.002 TYR K 92 ARG 0.011 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: K 174 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: K 225 GLU cc_start: 0.8037 (pt0) cc_final: 0.7546 (tp30) REVERT: G 67 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: G 74 LYS cc_start: 0.8219 (tptt) cc_final: 0.7956 (mmmt) REVERT: E 120 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8554 (mmm) REVERT: C 67 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7965 (tp30) outliers start: 35 outliers final: 20 residues processed: 185 average time/residue: 1.5790 time to fit residues: 312.4518 Evaluate side-chains 179 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 174 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.8514 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13858 Z= 0.191 Angle : 0.537 7.693 19738 Z= 0.322 Chirality : 0.035 0.141 2236 Planarity : 0.004 0.057 1658 Dihedral : 29.649 178.115 3828 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.08 % Allowed : 17.18 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 1009 helix: 1.89 (0.21), residues: 636 sheet: -0.13 (0.77), residues: 38 loop : -1.03 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.008 0.001 HIS K 149 PHE 0.007 0.001 PHE K 281 TYR 0.018 0.001 TYR H 84 ARG 0.010 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8013 (pt0) cc_final: 0.7442 (tp30) REVERT: G 67 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: G 74 LYS cc_start: 0.8232 (tptt) cc_final: 0.7998 (mmmt) REVERT: E 56 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8214 (ttpt) REVERT: C 67 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7931 (tp30) outliers start: 26 outliers final: 20 residues processed: 179 average time/residue: 1.6169 time to fit residues: 309.0630 Evaluate side-chains 184 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13858 Z= 0.181 Angle : 0.518 5.654 19738 Z= 0.312 Chirality : 0.034 0.146 2236 Planarity : 0.004 0.056 1658 Dihedral : 29.554 176.360 3828 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.49 % Allowed : 17.89 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1009 helix: 1.96 (0.21), residues: 635 sheet: -0.09 (0.76), residues: 38 loop : -1.00 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.006 0.001 HIS K 149 PHE 0.007 0.001 PHE F 61 TYR 0.026 0.001 TYR H 84 ARG 0.014 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8032 (pt0) cc_final: 0.7420 (tp30) REVERT: F 44 LYS cc_start: 0.8673 (mtpm) cc_final: 0.8463 (mtpt) REVERT: G 67 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: G 74 LYS cc_start: 0.8193 (tptt) cc_final: 0.7944 (mmmt) REVERT: E 56 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8163 (ttpt) REVERT: C 67 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7914 (tp30) outliers start: 21 outliers final: 16 residues processed: 174 average time/residue: 1.6441 time to fit residues: 305.1894 Evaluate side-chains 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8499 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.205 Angle : 0.510 5.203 19738 Z= 0.308 Chirality : 0.034 0.146 2236 Planarity : 0.004 0.044 1658 Dihedral : 29.426 177.608 3828 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.61 % Allowed : 17.89 % Favored : 79.50 % 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: 1.48 (0.27), residues: 1009 helix: 1.99 (0.21), residues: 640 sheet: -0.07 (0.76), residues: 38 loop : -0.91 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.018 0.001 TYR H 84 ARG 0.012 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8004 (pt0) cc_final: 0.7382 (tp30) REVERT: A 133 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: G 67 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: G 74 LYS cc_start: 0.8165 (tptt) cc_final: 0.7927 (mmmt) REVERT: E 56 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8190 (ttpt) REVERT: C 67 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7935 (tp30) REVERT: C 79 LYS cc_start: 0.8366 (mmtp) cc_final: 0.8151 (mmtm) outliers start: 22 outliers final: 17 residues processed: 177 average time/residue: 1.6246 time to fit residues: 306.9171 Evaluate side-chains 181 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 116 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: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13858 Z= 0.212 Angle : 0.523 9.426 19738 Z= 0.312 Chirality : 0.034 0.159 2236 Planarity : 0.004 0.053 1658 Dihedral : 29.423 177.548 3828 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.73 % Allowed : 18.48 % Favored : 78.79 % 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: 1.48 (0.27), residues: 1009 helix: 2.00 (0.21), residues: 637 sheet: -0.03 (0.76), residues: 38 loop : -0.92 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.025 0.002 TYR H 84 ARG 0.014 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8007 (pt0) cc_final: 0.7383 (tp30) REVERT: A 133 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: G 67 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: G 74 LYS cc_start: 0.8144 (tptt) cc_final: 0.7905 (mmmt) REVERT: E 56 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8177 (ttpt) REVERT: C 67 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7935 (tp30) outliers start: 23 outliers final: 17 residues processed: 172 average time/residue: 1.7125 time to fit residues: 313.6368 Evaluate side-chains 180 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.196 Angle : 0.519 8.711 19738 Z= 0.311 Chirality : 0.034 0.153 2236 Planarity : 0.004 0.056 1658 Dihedral : 29.423 177.565 3828 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.49 % Allowed : 18.60 % Favored : 78.91 % 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 (0.27), residues: 1009 helix: 2.01 (0.21), residues: 637 sheet: -0.04 (0.76), residues: 38 loop : -0.91 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS K 149 PHE 0.007 0.001 PHE F 61 TYR 0.031 0.002 TYR B 88 ARG 0.013 0.000 ARG C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8006 (pt0) cc_final: 0.7381 (tp30) REVERT: A 133 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: G 67 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7986 (tp30) REVERT: G 74 LYS cc_start: 0.8160 (tptt) cc_final: 0.7919 (mmmt) REVERT: E 56 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8174 (ttpt) REVERT: C 67 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7932 (tp30) outliers start: 21 outliers final: 17 residues processed: 172 average time/residue: 1.7040 time to fit residues: 311.9141 Evaluate side-chains 180 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.115923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081341 restraints weight = 24094.342| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.68 r_work: 0.3200 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13858 Z= 0.188 Angle : 0.517 8.562 19738 Z= 0.309 Chirality : 0.034 0.150 2236 Planarity : 0.004 0.055 1658 Dihedral : 29.421 177.589 3828 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.49 % Allowed : 18.72 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 1009 helix: 2.02 (0.21), residues: 637 sheet: -0.04 (0.76), residues: 38 loop : -0.90 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.030 0.002 TYR B 88 ARG 0.013 0.000 ARG C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5375.84 seconds wall clock time: 94 minutes 55.60 seconds (5695.60 seconds total)