Starting phenix.real_space_refine on Thu Sep 26 02:44:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2024/7y7i_33666.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2024/7y7i_33666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2024/7y7i_33666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2024/7y7i_33666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2024/7y7i_33666.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2024/7y7i_33666.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 286 5.49 5 S 14 5.16 5 C 6943 2.51 5 N 2341 2.21 5 O 2861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12445 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 845 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "B" 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: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 811 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 281 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "L" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 281 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Time building chain proxies: 7.05, per 1000 atoms: 0.57 Number of scatterers: 12445 At special positions: 0 Unit cell: (117.6, 111.72, 116.62, 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 286 15.00 O 2861 8.00 N 2341 7.00 C 6943 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 - 3.00 Amino acid : True - 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: 3.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 67.8% alpha, 3.6% beta 136 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 5.88 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 4.057A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 80 Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.684A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.629A pdb=" N LEU A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.901A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.684A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.694A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.607A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.987A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.707A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.558A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.553A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.691A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.978A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 80 removed outlier: 3.546A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.694A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.794A pdb=" N LEU E 126 " --> pdb=" O TYR E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.615A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.812A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.836A pdb=" N ALA G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.410A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 98 removed outlier: 4.103A pdb=" N LEU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.605A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.793A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 534 through 538 Processing helix chain 'L' and resid 534 through 538 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.594A pdb=" N ARG A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.559A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.636A pdb=" N ARG C 43 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.560A pdb=" N ILE C 79 " --> pdb=" O GLY D 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.818A pdb=" N ARG E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.584A pdb=" N ARG G 43 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 541 through 543 Processing sheet with id=AB3, first strand: chain 'L' and resid 540 through 542 393 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 3.52 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: 2513 1.33 - 1.45: 4151 1.45 - 1.57: 6002 1.57 - 1.69: 570 1.69 - 1.81: 22 Bond restraints: 13258 Sorted by residual: bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" C3' DC J 192 " pdb=" O3' DC J 192 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" C3' DC J 178 " pdb=" O3' DC J 178 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" C1' DT I 103 " pdb=" N1 DT I 103 " ideal model delta sigma weight residual 1.490 1.525 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" C3' DC J 242 " pdb=" C2' DC J 242 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 13253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 18584 1.58 - 3.15: 510 3.15 - 4.73: 32 4.73 - 6.30: 7 6.30 - 7.88: 2 Bond angle restraints: 19135 Sorted by residual: angle pdb=" C3' DC J 190 " pdb=" C2' DC J 190 " pdb=" C1' DC J 190 " ideal model delta sigma weight residual 101.60 96.94 4.66 1.50e+00 4.44e-01 9.65e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 104.82 7.88 3.00e+00 1.11e-01 6.90e+00 angle pdb=" C ASN G 111 " pdb=" CA ASN G 111 " pdb=" CB ASN G 111 " ideal model delta sigma weight residual 109.68 114.86 -5.18 1.98e+00 2.55e-01 6.84e+00 angle pdb=" C3' DC J 192 " pdb=" O3' DC J 192 " pdb=" P DC J 193 " ideal model delta sigma weight residual 120.20 123.84 -3.64 1.50e+00 4.44e-01 5.89e+00 angle pdb=" C4' DG I 66 " pdb=" C3' DG I 66 " pdb=" C2' DG I 66 " ideal model delta sigma weight residual 102.40 98.79 3.61 1.50e+00 4.44e-01 5.81e+00 ... (remaining 19130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 5122 25.68 - 51.37: 1590 51.37 - 77.05: 472 77.05 - 102.73: 26 102.73 - 128.41: 2 Dihedral angle restraints: 7212 sinusoidal: 4834 harmonic: 2378 Sorted by residual: dihedral pdb=" C4' DC J 178 " pdb=" C3' DC J 178 " pdb=" O3' DC J 178 " pdb=" P DT J 179 " ideal model delta sinusoidal sigma weight residual -140.00 -11.59 -128.41 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DC J 192 " pdb=" C3' DC J 192 " pdb=" O3' DC J 192 " pdb=" P DC J 193 " ideal model delta sinusoidal sigma weight residual -140.00 -13.98 -126.02 1 3.50e+01 8.16e-04 1.24e+01 dihedral pdb=" CA ARG E 80 " pdb=" C ARG E 80 " pdb=" N GLY E 81 " pdb=" CA GLY E 81 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1519 0.032 - 0.064: 478 0.064 - 0.095: 117 0.095 - 0.127: 46 0.127 - 0.159: 5 Chirality restraints: 2165 Sorted by residual: chirality pdb=" C3' DC J 191 " pdb=" C4' DC J 191 " pdb=" O3' DC J 191 " pdb=" C2' DC J 191 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C3' DC J 190 " pdb=" C4' DC J 190 " pdb=" O3' DC J 190 " pdb=" C2' DC J 190 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE G 112 " pdb=" N ILE G 112 " pdb=" C ILE G 112 " pdb=" CB ILE G 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 2162 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 162 " -0.016 2.00e-02 2.50e+03 1.52e-02 6.92e+00 pdb=" N9 DG J 162 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG J 162 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG J 162 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J 162 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG J 162 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG J 162 " -0.034 2.00e-02 2.50e+03 pdb=" N2 DG J 162 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 162 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 530 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO K 531 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 531 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 531 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 63 " -0.006 2.00e-02 2.50e+03 1.30e-02 3.80e+00 pdb=" N1 DC I 63 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DC I 63 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC I 63 " 0.021 2.00e-02 2.50e+03 pdb=" N3 DC I 63 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 63 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 63 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC I 63 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 63 " 0.004 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1936 2.77 - 3.30: 11063 3.30 - 3.83: 23605 3.83 - 4.37: 26505 4.37 - 4.90: 40152 Nonbonded interactions: 103261 Sorted by model distance: nonbonded pdb=" OG1 THR L 523 " pdb=" OG SER L 525 " model vdw 2.234 3.040 nonbonded pdb=" NH2 ARG A 40 " pdb=" O2 DT J 227 " model vdw 2.242 3.120 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 78 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 40 " pdb=" OE1 GLU D 71 " model vdw 2.296 3.040 nonbonded pdb=" N2 DG I 127 " pdb=" N3 DC J 164 " model vdw 2.305 3.200 ... (remaining 103256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 123) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 0.430 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.910 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 0.038 13258 Z= 0.193 Angle : 0.571 7.878 19135 Z= 0.342 Chirality : 0.036 0.159 2165 Planarity : 0.004 0.060 1429 Dihedral : 28.764 128.413 5684 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.15 % Allowed : 14.85 % Favored : 85.01 % 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: 2.18 (0.30), residues: 804 helix: 2.59 (0.23), residues: 511 sheet: -2.85 (0.88), residues: 26 loop : -0.40 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 536 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE E 78 TYR 0.031 0.001 TYR B 88 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.915 Fit side-chains REVERT: B 91 LYS cc_start: 0.8317 (tttt) cc_final: 0.7880 (tmtt) REVERT: C 21 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7973 (mmm-85) REVERT: C 96 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7839 (mtmm) REVERT: D 99 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8070 (mtm-85) REVERT: D 119 THR cc_start: 0.8233 (m) cc_final: 0.7866 (p) REVERT: E 42 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7364 (mtp180) REVERT: E 77 LEU cc_start: 0.8318 (tt) cc_final: 0.8055 (tp) REVERT: E 89 MET cc_start: 0.7559 (mmm) cc_final: 0.7159 (mmt) REVERT: F 29 ILE cc_start: 0.8516 (mp) cc_final: 0.8231 (mm) REVERT: F 79 LYS cc_start: 0.8403 (mttp) cc_final: 0.8168 (mmtp) REVERT: H 34 LYS cc_start: 0.7799 (tptt) cc_final: 0.6514 (mttt) REVERT: L 544 ASP cc_start: 0.7010 (p0) cc_final: 0.6723 (m-30) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.4594 time to fit residues: 90.1516 Evaluate side-chains 98 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 25 GLN D 82 HIS H 49 HIS K 548 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13258 Z= 0.243 Angle : 0.611 7.947 19135 Z= 0.361 Chirality : 0.038 0.164 2165 Planarity : 0.005 0.055 1429 Dihedral : 31.457 128.119 4056 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.46 % Allowed : 14.99 % Favored : 83.55 % 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: 2.32 (0.29), residues: 804 helix: 2.56 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.46 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 536 HIS 0.006 0.001 HIS D 82 PHE 0.010 0.002 PHE A 101 TYR 0.037 0.002 TYR B 88 ARG 0.007 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.946 Fit side-chains REVERT: A 111 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7968 (mp) REVERT: B 91 LYS cc_start: 0.8492 (tttt) cc_final: 0.7959 (tmtt) REVERT: C 65 GLU cc_start: 0.8321 (tt0) cc_final: 0.7919 (tt0) REVERT: C 96 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7848 (mtmm) REVERT: C 105 GLN cc_start: 0.8038 (mt0) cc_final: 0.7778 (mm-40) REVERT: D 99 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8120 (mtm-85) REVERT: D 119 THR cc_start: 0.8317 (m) cc_final: 0.7839 (p) REVERT: E 48 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8562 (mm) REVERT: E 89 MET cc_start: 0.7633 (mmm) cc_final: 0.7124 (mmt) REVERT: E 108 ASP cc_start: 0.7915 (m-30) cc_final: 0.7692 (m-30) REVERT: F 79 LYS cc_start: 0.8454 (mttp) cc_final: 0.8092 (mmtp) REVERT: F 95 ARG cc_start: 0.8272 (mtt90) cc_final: 0.8004 (ptp90) REVERT: G 65 GLU cc_start: 0.7784 (tp30) cc_final: 0.7291 (tt0) REVERT: H 34 LYS cc_start: 0.7592 (tptt) cc_final: 0.6349 (mttt) outliers start: 10 outliers final: 4 residues processed: 103 average time/residue: 0.3750 time to fit residues: 49.9390 Evaluate side-chains 88 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13258 Z= 0.313 Angle : 0.667 7.778 19135 Z= 0.394 Chirality : 0.042 0.195 2165 Planarity : 0.006 0.067 1429 Dihedral : 31.699 121.690 4056 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.62 % Allowed : 14.12 % Favored : 83.26 % 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: 2.01 (0.29), residues: 804 helix: 2.42 (0.22), residues: 520 sheet: -2.38 (1.32), residues: 20 loop : -0.62 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 536 HIS 0.004 0.001 HIS H 49 PHE 0.014 0.002 PHE C 26 TYR 0.027 0.002 TYR B 88 ARG 0.007 0.001 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.992 Fit side-chains REVERT: A 111 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 91 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8055 (ttpp) REVERT: C 65 GLU cc_start: 0.8262 (tt0) cc_final: 0.7819 (tt0) REVERT: C 93 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: C 109 LEU cc_start: 0.8673 (mt) cc_final: 0.8425 (mp) REVERT: D 99 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8317 (mtm-85) REVERT: D 113 GLU cc_start: 0.7936 (tt0) cc_final: 0.7627 (tp30) REVERT: E 48 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8553 (mm) REVERT: E 53 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7540 (ttp-110) REVERT: E 89 MET cc_start: 0.7681 (mmm) cc_final: 0.6981 (mmt) REVERT: F 79 LYS cc_start: 0.8423 (mttp) cc_final: 0.8019 (mmtp) REVERT: G 65 GLU cc_start: 0.7854 (tp30) cc_final: 0.7477 (tp30) REVERT: G 73 ASP cc_start: 0.7781 (m-30) cc_final: 0.7547 (m-30) REVERT: H 34 LYS cc_start: 0.7479 (tptt) cc_final: 0.6213 (mtpt) REVERT: K 521 ILE cc_start: 0.3901 (OUTLIER) cc_final: 0.3287 (mm) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 0.3757 time to fit residues: 53.1742 Evaluate side-chains 97 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain K residue 521 ILE Chi-restraints excluded: chain K residue 534 SER Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.0060 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.3802 ------------------------------------------------------------------------------- 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: 0.7735 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13258 Z= 0.313 Angle : 0.650 6.277 19135 Z= 0.386 Chirality : 0.041 0.178 2165 Planarity : 0.005 0.057 1429 Dihedral : 31.568 121.459 4056 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.62 % Allowed : 16.74 % Favored : 80.64 % 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: 1.89 (0.30), residues: 804 helix: 2.34 (0.22), residues: 523 sheet: -2.65 (1.24), residues: 20 loop : -0.70 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 536 HIS 0.003 0.001 HIS A 115 PHE 0.013 0.002 PHE A 101 TYR 0.022 0.002 TYR B 88 ARG 0.004 0.001 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.866 Fit side-chains REVERT: A 111 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7934 (mp) REVERT: B 91 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8033 (ttpp) REVERT: C 65 GLU cc_start: 0.8319 (tt0) cc_final: 0.7912 (tt0) REVERT: C 93 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: D 99 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8295 (mtm-85) REVERT: D 113 GLU cc_start: 0.7902 (tt0) cc_final: 0.7571 (tp30) REVERT: E 48 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8469 (mm) REVERT: E 53 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7564 (ttp-110) REVERT: E 89 MET cc_start: 0.7723 (mmm) cc_final: 0.7030 (mmt) REVERT: E 117 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6534 (mtm110) REVERT: E 133 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7389 (ptt180) REVERT: F 79 LYS cc_start: 0.8444 (mttp) cc_final: 0.8004 (mmtp) REVERT: H 34 LYS cc_start: 0.7431 (tptt) cc_final: 0.6200 (mtpt) REVERT: K 521 ILE cc_start: 0.4256 (OUTLIER) cc_final: 0.3749 (mm) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.4184 time to fit residues: 53.7442 Evaluate side-chains 99 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 521 ILE Chi-restraints excluded: chain K residue 534 SER Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13258 Z= 0.301 Angle : 0.642 6.092 19135 Z= 0.382 Chirality : 0.041 0.176 2165 Planarity : 0.005 0.061 1429 Dihedral : 31.571 121.129 4056 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.64 % Allowed : 16.01 % Favored : 80.35 % 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: 1.92 (0.30), residues: 804 helix: 2.35 (0.22), residues: 524 sheet: -2.63 (1.20), residues: 20 loop : -0.68 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 86 HIS 0.003 0.001 HIS A 115 PHE 0.013 0.002 PHE A 101 TYR 0.016 0.002 TYR B 88 ARG 0.004 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 1.148 Fit side-chains REVERT: A 111 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 91 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8022 (ttpp) REVERT: C 65 GLU cc_start: 0.8256 (tt0) cc_final: 0.7817 (tt0) REVERT: C 93 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: D 99 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8355 (mtm-85) REVERT: D 113 GLU cc_start: 0.7890 (tt0) cc_final: 0.7566 (tp30) REVERT: E 48 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8532 (mm) REVERT: E 53 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7549 (ttp-110) REVERT: E 59 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: E 89 MET cc_start: 0.7724 (mmm) cc_final: 0.7019 (mmt) REVERT: E 117 ARG cc_start: 0.6839 (mtm110) cc_final: 0.6596 (mtm110) REVERT: E 133 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7475 (ptt180) REVERT: F 79 LYS cc_start: 0.8462 (mttp) cc_final: 0.8013 (mmtp) REVERT: G 65 GLU cc_start: 0.8000 (tp30) cc_final: 0.7298 (tp30) REVERT: H 34 LYS cc_start: 0.7503 (tptt) cc_final: 0.6218 (mtpt) REVERT: H 113 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: K 521 ILE cc_start: 0.4691 (OUTLIER) cc_final: 0.4250 (mm) outliers start: 25 outliers final: 16 residues processed: 103 average time/residue: 0.3983 time to fit residues: 53.0758 Evaluate side-chains 102 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain K residue 521 ILE Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13258 Z= 0.219 Angle : 0.597 6.037 19135 Z= 0.361 Chirality : 0.039 0.175 2165 Planarity : 0.004 0.050 1429 Dihedral : 31.477 122.832 4056 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.06 % Allowed : 17.03 % Favored : 79.91 % 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: 2.16 (0.30), residues: 804 helix: 2.55 (0.22), residues: 524 sheet: -2.51 (1.25), residues: 20 loop : -0.64 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 536 HIS 0.002 0.001 HIS A 115 PHE 0.014 0.001 PHE L 535 TYR 0.015 0.001 TYR B 88 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.091 Fit side-chains REVERT: A 111 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7969 (mp) REVERT: B 91 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8019 (ttpp) REVERT: C 65 GLU cc_start: 0.8245 (tt0) cc_final: 0.7814 (tt0) REVERT: C 93 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: D 99 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8209 (mtm-85) REVERT: E 48 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8467 (mm) REVERT: E 53 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7545 (ttp-110) REVERT: E 59 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: E 89 MET cc_start: 0.7617 (mmm) cc_final: 0.6952 (mmt) REVERT: E 108 ASP cc_start: 0.7808 (m-30) cc_final: 0.7507 (m-30) REVERT: E 117 ARG cc_start: 0.6788 (mtm110) cc_final: 0.6546 (mtm110) REVERT: E 133 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7361 (ptt180) REVERT: F 79 LYS cc_start: 0.8457 (mttp) cc_final: 0.8000 (mmtp) REVERT: G 65 GLU cc_start: 0.8011 (tp30) cc_final: 0.7296 (tp30) REVERT: G 72 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7011 (ttm170) REVERT: G 93 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7859 (mm-30) REVERT: H 34 LYS cc_start: 0.7488 (tptt) cc_final: 0.6237 (mtpt) REVERT: H 113 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: K 521 ILE cc_start: 0.4740 (OUTLIER) cc_final: 0.4311 (mm) outliers start: 21 outliers final: 10 residues processed: 98 average time/residue: 0.4060 time to fit residues: 50.8633 Evaluate side-chains 96 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain K residue 521 ILE Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.7671 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13258 Z= 0.196 Angle : 0.569 6.294 19135 Z= 0.345 Chirality : 0.037 0.175 2165 Planarity : 0.004 0.046 1429 Dihedral : 31.291 124.039 4056 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.47 % Allowed : 17.90 % 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: 2.44 (0.30), residues: 804 helix: 2.75 (0.22), residues: 524 sheet: -1.98 (1.32), residues: 20 loop : -0.51 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 536 HIS 0.002 0.001 HIS A 115 PHE 0.008 0.001 PHE A 101 TYR 0.012 0.001 TYR B 88 ARG 0.004 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.927 Fit side-chains REVERT: A 111 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7926 (mp) REVERT: B 91 LYS cc_start: 0.8441 (ttpt) cc_final: 0.7921 (tmtt) REVERT: C 65 GLU cc_start: 0.8275 (tt0) cc_final: 0.7841 (tt0) REVERT: C 93 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: D 99 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8347 (mtm-85) REVERT: E 48 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8447 (mm) REVERT: E 53 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7510 (ttp-110) REVERT: E 59 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8382 (pm20) REVERT: E 89 MET cc_start: 0.7589 (mmm) cc_final: 0.6897 (mmt) REVERT: E 108 ASP cc_start: 0.7762 (m-30) cc_final: 0.7448 (m-30) REVERT: E 133 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7166 (ptt180) REVERT: F 79 LYS cc_start: 0.8474 (mttp) cc_final: 0.7925 (mmtp) REVERT: G 65 GLU cc_start: 0.7984 (tp30) cc_final: 0.7295 (tp30) REVERT: G 72 ARG cc_start: 0.7281 (mtm110) cc_final: 0.6961 (ttm170) REVERT: H 34 LYS cc_start: 0.7462 (tptt) cc_final: 0.6219 (mtpt) REVERT: H 113 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7701 (tp30) outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.4208 time to fit residues: 51.5179 Evaluate side-chains 94 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13258 Z= 0.286 Angle : 0.625 6.252 19135 Z= 0.372 Chirality : 0.040 0.170 2165 Planarity : 0.005 0.057 1429 Dihedral : 31.458 124.082 4056 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.77 % Allowed : 17.76 % Favored : 79.48 % 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: 2.19 (0.30), residues: 804 helix: 2.53 (0.22), residues: 524 sheet: -1.82 (1.33), residues: 20 loop : -0.56 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 86 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.002 PHE A 101 TYR 0.012 0.002 TYR B 51 ARG 0.004 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.949 Fit side-chains REVERT: A 111 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 91 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8020 (ttpp) REVERT: C 65 GLU cc_start: 0.8261 (tt0) cc_final: 0.7826 (tt0) REVERT: C 93 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: D 99 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8319 (mtm-85) REVERT: D 113 GLU cc_start: 0.7821 (tt0) cc_final: 0.7481 (tp30) REVERT: E 48 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8488 (mm) REVERT: E 53 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7541 (ttp-110) REVERT: E 59 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: E 89 MET cc_start: 0.7653 (mmm) cc_final: 0.6940 (mmt) REVERT: E 108 ASP cc_start: 0.7826 (m-30) cc_final: 0.7526 (m-30) REVERT: E 133 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7348 (ptt180) REVERT: F 79 LYS cc_start: 0.8515 (mttp) cc_final: 0.8060 (mmtp) REVERT: G 65 GLU cc_start: 0.8024 (tp30) cc_final: 0.7306 (tp30) REVERT: H 34 LYS cc_start: 0.7503 (tptt) cc_final: 0.6228 (mtpt) REVERT: H 113 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7822 (tp30) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.3814 time to fit residues: 48.5094 Evaluate side-chains 100 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13258 Z= 0.244 Angle : 0.603 6.096 19135 Z= 0.362 Chirality : 0.039 0.172 2165 Planarity : 0.004 0.046 1429 Dihedral : 31.426 124.406 4056 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.62 % Allowed : 18.34 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.30), residues: 804 helix: 2.55 (0.22), residues: 524 sheet: -1.68 (1.32), residues: 20 loop : -0.55 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 86 HIS 0.002 0.001 HIS A 115 PHE 0.014 0.002 PHE L 535 TYR 0.011 0.001 TYR B 88 ARG 0.003 0.000 ARG L 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.744 Fit side-chains REVERT: A 111 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 91 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8021 (ttpp) REVERT: C 65 GLU cc_start: 0.8273 (tt0) cc_final: 0.7823 (tt0) REVERT: C 93 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: D 99 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.8307 (mtm-85) REVERT: E 48 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8467 (mm) REVERT: E 53 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7555 (ttp-110) REVERT: E 59 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: E 89 MET cc_start: 0.7649 (mmm) cc_final: 0.6938 (mmt) REVERT: E 108 ASP cc_start: 0.7811 (m-30) cc_final: 0.7509 (m-30) REVERT: E 133 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7322 (ptt180) REVERT: F 79 LYS cc_start: 0.8490 (mttp) cc_final: 0.7989 (mmtp) REVERT: G 65 GLU cc_start: 0.8020 (tp30) cc_final: 0.7283 (tp30) REVERT: G 72 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7057 (ttm170) REVERT: H 34 LYS cc_start: 0.7482 (tptt) cc_final: 0.6228 (mtpt) REVERT: H 113 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7817 (tp30) outliers start: 18 outliers final: 12 residues processed: 92 average time/residue: 0.4055 time to fit residues: 47.4917 Evaluate side-chains 95 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.7739 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13258 Z= 0.301 Angle : 0.643 5.919 19135 Z= 0.383 Chirality : 0.041 0.177 2165 Planarity : 0.005 0.054 1429 Dihedral : 31.603 124.236 4056 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.35 % Allowed : 17.61 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.30), residues: 804 helix: 2.40 (0.22), residues: 525 sheet: -1.76 (1.28), residues: 20 loop : -0.65 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 536 HIS 0.002 0.001 HIS E 115 PHE 0.013 0.002 PHE A 101 TYR 0.012 0.002 TYR B 51 ARG 0.004 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.849 Fit side-chains REVERT: A 111 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8029 (mp) REVERT: B 91 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8008 (ttpp) REVERT: C 65 GLU cc_start: 0.8260 (tt0) cc_final: 0.7811 (tt0) REVERT: C 93 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: D 99 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8407 (mtm-85) REVERT: D 113 GLU cc_start: 0.7785 (tt0) cc_final: 0.7500 (tp30) REVERT: E 48 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8490 (mm) REVERT: E 53 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7576 (ttp-110) REVERT: E 59 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: E 89 MET cc_start: 0.7681 (mmm) cc_final: 0.6967 (mmt) REVERT: E 133 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7373 (ptt180) REVERT: F 79 LYS cc_start: 0.8536 (mttp) cc_final: 0.8269 (mmtp) REVERT: G 65 GLU cc_start: 0.8058 (tp30) cc_final: 0.7343 (tp30) REVERT: H 34 LYS cc_start: 0.7469 (tptt) cc_final: 0.6217 (mtpt) REVERT: H 113 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7856 (tp30) outliers start: 23 outliers final: 16 residues processed: 97 average time/residue: 0.4051 time to fit residues: 50.4969 Evaluate side-chains 100 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain K residue 534 SER Chi-restraints excluded: chain L residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 10 optimal weight: 0.0000 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.177778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140825 restraints weight = 14902.232| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.90 r_work: 0.3180 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13258 Z= 0.163 Angle : 0.543 6.284 19135 Z= 0.330 Chirality : 0.035 0.178 2165 Planarity : 0.004 0.045 1429 Dihedral : 31.176 128.000 4056 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 18.92 % Favored : 79.18 % 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: 2.55 (0.30), residues: 804 helix: 2.83 (0.22), residues: 525 sheet: -1.62 (1.25), residues: 20 loop : -0.50 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.002 0.001 HIS A 115 PHE 0.008 0.001 PHE L 535 TYR 0.010 0.001 TYR B 88 ARG 0.004 0.000 ARG L 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.64 seconds wall clock time: 38 minutes 44.69 seconds (2324.69 seconds total)