Starting phenix.real_space_refine on Thu Feb 15 13:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6q_28888/02_2024/8f6q_28888.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6q_28888/02_2024/8f6q_28888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6q_28888/02_2024/8f6q_28888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6q_28888/02_2024/8f6q_28888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6q_28888/02_2024/8f6q_28888.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6q_28888/02_2024/8f6q_28888.pdb" } resolution = 3.6 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= 0.001 sd= 0.084 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 7936 2.51 5 N 2120 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "F GLU 2": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "G GLU 2": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "H GLU 2": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12352 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain: "B" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain: "C" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain: "F" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain: "H" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1544 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Time building chain proxies: 6.68, per 1000 atoms: 0.54 Number of scatterers: 12352 At special positions: 0 Unit cell: (135.763, 135.763, 53.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 2280 8.00 N 2120 7.00 C 7936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.30 Conformation dependent library (CDL) restraints added in 2.0 seconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 98.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 1 through 22 Processing helix chain 'A' and resid 24 through 48 Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.071A pdb=" N VAL A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 99 removed outlier: 4.139A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 122 removed outlier: 3.927A pdb=" N VAL A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 149 Processing helix chain 'A' and resid 151 through 172 removed outlier: 3.781A pdb=" N GLU A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 199 Processing helix chain 'B' and resid 2 through 22 Processing helix chain 'B' and resid 24 through 48 Processing helix chain 'B' and resid 50 through 72 removed outlier: 4.071A pdb=" N VAL B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 99 removed outlier: 4.139A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 122 removed outlier: 3.927A pdb=" N VAL B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 149 Processing helix chain 'B' and resid 151 through 172 removed outlier: 3.781A pdb=" N GLU B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 199 Processing helix chain 'C' and resid 2 through 22 Processing helix chain 'C' and resid 24 through 48 Processing helix chain 'C' and resid 50 through 72 removed outlier: 4.071A pdb=" N VAL C 54 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 99 removed outlier: 4.139A pdb=" N LYS C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 122 removed outlier: 3.927A pdb=" N VAL C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 149 Processing helix chain 'C' and resid 151 through 172 removed outlier: 3.782A pdb=" N GLU C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 199 Processing helix chain 'D' and resid 2 through 22 Processing helix chain 'D' and resid 24 through 48 Processing helix chain 'D' and resid 50 through 72 removed outlier: 4.071A pdb=" N VAL D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 99 removed outlier: 4.139A pdb=" N LYS D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 122 removed outlier: 3.926A pdb=" N VAL D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 149 Processing helix chain 'D' and resid 151 through 172 removed outlier: 3.781A pdb=" N GLU D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 199 Processing helix chain 'E' and resid 2 through 22 Processing helix chain 'E' and resid 24 through 48 Processing helix chain 'E' and resid 50 through 72 removed outlier: 4.071A pdb=" N VAL E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 99 removed outlier: 4.140A pdb=" N LYS E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 122 removed outlier: 3.926A pdb=" N VAL E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 149 Processing helix chain 'E' and resid 151 through 172 removed outlier: 3.781A pdb=" N GLU E 155 " --> pdb=" O PRO E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 199 Processing helix chain 'F' and resid 2 through 22 Processing helix chain 'F' and resid 24 through 48 Processing helix chain 'F' and resid 50 through 72 removed outlier: 4.071A pdb=" N VAL F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 99 removed outlier: 4.139A pdb=" N LYS F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 122 removed outlier: 3.927A pdb=" N VAL F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 149 Processing helix chain 'F' and resid 151 through 172 removed outlier: 3.781A pdb=" N GLU F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 199 Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'G' and resid 24 through 48 Processing helix chain 'G' and resid 50 through 72 removed outlier: 4.070A pdb=" N VAL G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 99 removed outlier: 4.139A pdb=" N LYS G 79 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 122 removed outlier: 3.927A pdb=" N VAL G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 149 Processing helix chain 'G' and resid 151 through 172 removed outlier: 3.781A pdb=" N GLU G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 199 Processing helix chain 'H' and resid 2 through 22 Processing helix chain 'H' and resid 24 through 48 Processing helix chain 'H' and resid 50 through 72 removed outlier: 4.071A pdb=" N VAL H 54 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 99 removed outlier: 4.140A pdb=" N LYS H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 removed outlier: 3.926A pdb=" N VAL H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 149 Processing helix chain 'H' and resid 151 through 172 removed outlier: 3.781A pdb=" N GLU H 155 " --> pdb=" O PRO H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 199 1273 hydrogen bonds defined for protein. 3819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3054 1.33 - 1.45: 2025 1.45 - 1.57: 7417 1.57 - 1.68: 0 1.68 - 1.80: 32 Bond restraints: 12528 Sorted by residual: bond pdb=" N ALA A 68 " pdb=" CA ALA A 68 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.21e-02 6.83e+03 8.10e+00 bond pdb=" N ALA G 68 " pdb=" CA ALA G 68 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.21e-02 6.83e+03 7.88e+00 bond pdb=" N ALA H 68 " pdb=" CA ALA H 68 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.21e-02 6.83e+03 7.83e+00 bond pdb=" N ALA C 68 " pdb=" CA ALA C 68 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.21e-02 6.83e+03 7.80e+00 bond pdb=" N ALA F 68 " pdb=" CA ALA F 68 " ideal model delta sigma weight residual 1.459 1.426 0.033 1.21e-02 6.83e+03 7.64e+00 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 208 106.95 - 113.71: 7328 113.71 - 120.48: 5022 120.48 - 127.25: 4218 127.25 - 134.01: 112 Bond angle restraints: 16888 Sorted by residual: angle pdb=" CA LEU C 67 " pdb=" CB LEU C 67 " pdb=" CG LEU C 67 " ideal model delta sigma weight residual 116.30 100.46 15.84 3.50e+00 8.16e-02 2.05e+01 angle pdb=" CA LEU A 67 " pdb=" CB LEU A 67 " pdb=" CG LEU A 67 " ideal model delta sigma weight residual 116.30 100.47 15.83 3.50e+00 8.16e-02 2.05e+01 angle pdb=" CA LEU H 67 " pdb=" CB LEU H 67 " pdb=" CG LEU H 67 " ideal model delta sigma weight residual 116.30 100.47 15.83 3.50e+00 8.16e-02 2.05e+01 angle pdb=" CA LEU G 67 " pdb=" CB LEU G 67 " pdb=" CG LEU G 67 " ideal model delta sigma weight residual 116.30 100.48 15.82 3.50e+00 8.16e-02 2.04e+01 angle pdb=" CA LEU B 67 " pdb=" CB LEU B 67 " pdb=" CG LEU B 67 " ideal model delta sigma weight residual 116.30 100.48 15.82 3.50e+00 8.16e-02 2.04e+01 ... (remaining 16883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7015 17.82 - 35.63: 601 35.63 - 53.45: 88 53.45 - 71.26: 8 71.26 - 89.08: 8 Dihedral angle restraints: 7720 sinusoidal: 3080 harmonic: 4640 Sorted by residual: dihedral pdb=" CB GLU H 17 " pdb=" CG GLU H 17 " pdb=" CD GLU H 17 " pdb=" OE1 GLU H 17 " ideal model delta sinusoidal sigma weight residual 0.00 -89.08 89.08 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU D 17 " pdb=" CG GLU D 17 " pdb=" CD GLU D 17 " pdb=" OE1 GLU D 17 " ideal model delta sinusoidal sigma weight residual 0.00 -89.07 89.07 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 17 " pdb=" CG GLU E 17 " pdb=" CD GLU E 17 " pdb=" OE1 GLU E 17 " ideal model delta sinusoidal sigma weight residual 0.00 -89.05 89.05 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1596 0.046 - 0.093: 284 0.093 - 0.139: 40 0.139 - 0.186: 0 0.186 - 0.232: 16 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CG LEU B 67 " pdb=" CB LEU B 67 " pdb=" CD1 LEU B 67 " pdb=" CD2 LEU B 67 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU C 67 " pdb=" CB LEU C 67 " pdb=" CD1 LEU C 67 " pdb=" CD2 LEU C 67 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU H 67 " pdb=" CB LEU H 67 " pdb=" CD1 LEU H 67 " pdb=" CD2 LEU H 67 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1933 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 66 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C GLU A 66 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU A 66 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 67 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 66 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C GLU D 66 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU D 66 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 67 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 66 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C GLU F 66 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU F 66 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU F 67 " 0.009 2.00e-02 2.50e+03 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 408 2.70 - 3.25: 13632 3.25 - 3.80: 21466 3.80 - 4.35: 23153 4.35 - 4.90: 39479 Nonbonded interactions: 98138 Sorted by model distance: nonbonded pdb=" NZ LYS C 139 " pdb=" OE2 GLU D 66 " model vdw 2.155 2.520 nonbonded pdb=" NZ LYS B 139 " pdb=" OE2 GLU C 66 " model vdw 2.180 2.520 nonbonded pdb=" OE1 GLU F 13 " pdb=" NH2 ARG F 16 " model vdw 2.207 2.520 nonbonded pdb=" OE1 GLU H 13 " pdb=" NH2 ARG H 16 " model vdw 2.208 2.520 nonbonded pdb=" OE1 GLU G 13 " pdb=" NH2 ARG G 16 " model vdw 2.208 2.520 ... (remaining 98133 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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 group one per residue 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: 0.520 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: 2.490 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.010 Find NCS groups from input model: 0.850 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12528 Z= 0.395 Angle : 0.724 15.844 16888 Z= 0.418 Chirality : 0.040 0.232 1936 Planarity : 0.003 0.028 2152 Dihedral : 12.978 89.081 4664 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 1576 helix: 0.67 (0.12), residues: 1480 sheet: None (None), residues: 0 loop : -3.60 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 113 PHE 0.006 0.001 PHE F 171 ARG 0.001 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.520 Fit side-chains REVERT: A 7 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7280 (mmp-170) REVERT: A 48 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 50 ASP cc_start: 0.7753 (t0) cc_final: 0.7519 (t70) REVERT: A 136 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 146 MET cc_start: 0.8025 (tpt) cc_final: 0.7790 (tpt) REVERT: A 173 ASP cc_start: 0.8326 (t0) cc_final: 0.8026 (t0) REVERT: B 6 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 7 ARG cc_start: 0.7719 (mtm180) cc_final: 0.7298 (mpt180) REVERT: B 48 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 136 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 7 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7311 (mmp-170) REVERT: C 48 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 136 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 146 MET cc_start: 0.7896 (tpt) cc_final: 0.7676 (tpt) REVERT: C 173 ASP cc_start: 0.8238 (t0) cc_final: 0.7964 (t0) REVERT: D 7 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7424 (mpt180) REVERT: D 48 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 136 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 142 MET cc_start: 0.9079 (tpp) cc_final: 0.8551 (tpt) REVERT: D 183 PHE cc_start: 0.8831 (t80) cc_final: 0.8565 (t80) REVERT: E 6 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8112 (mm-30) REVERT: E 7 ARG cc_start: 0.7548 (mtm180) cc_final: 0.7246 (mmp-170) REVERT: E 48 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7507 (mm-30) REVERT: E 136 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8016 (tm-30) REVERT: E 142 MET cc_start: 0.9067 (tpp) cc_final: 0.8657 (tpt) REVERT: E 146 MET cc_start: 0.8033 (tpt) cc_final: 0.7749 (tpt) REVERT: F 6 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 7 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7286 (mpt180) REVERT: F 48 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7518 (mm-30) REVERT: F 136 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7868 (tm-30) REVERT: F 183 PHE cc_start: 0.8781 (t80) cc_final: 0.8580 (t80) REVERT: G 6 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8118 (mm-30) REVERT: G 7 ARG cc_start: 0.7404 (mtm180) cc_final: 0.7036 (mmp-170) REVERT: G 48 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7396 (mm-30) REVERT: G 136 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7999 (tm-30) REVERT: H 7 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7419 (mpt180) REVERT: H 48 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7534 (mm-30) REVERT: H 136 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7862 (tm-30) REVERT: H 142 MET cc_start: 0.9041 (tpp) cc_final: 0.8629 (tpt) REVERT: H 173 ASP cc_start: 0.8135 (t0) cc_final: 0.7933 (t0) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.3890 time to fit residues: 177.6084 Evaluate side-chains 161 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN E 71 ASN F 71 ASN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12528 Z= 0.238 Angle : 0.540 8.506 16888 Z= 0.281 Chirality : 0.033 0.164 1936 Planarity : 0.003 0.029 2152 Dihedral : 3.402 13.078 1688 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.20 % Allowed : 8.70 % Favored : 89.10 % 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: 2.71 (0.20), residues: 1576 helix: 2.06 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -2.24 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 113 PHE 0.015 0.001 PHE H 183 ARG 0.005 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 7 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7264 (mmp-170) REVERT: A 136 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 6 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7379 (mm-30) REVERT: B 7 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7185 (mmp-170) REVERT: B 24 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 47 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7159 (ttmm) REVERT: B 48 GLU cc_start: 0.7919 (mm-30) cc_final: 0.6763 (mp0) REVERT: B 136 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 136 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7871 (tm-30) REVERT: C 142 MET cc_start: 0.9077 (tpp) cc_final: 0.8734 (tpt) REVERT: D 7 ARG cc_start: 0.7749 (mtm180) cc_final: 0.7483 (mpt180) REVERT: D 136 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 142 MET cc_start: 0.9112 (tpp) cc_final: 0.8563 (tpt) REVERT: E 6 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8064 (mm-30) REVERT: E 7 ARG cc_start: 0.7532 (mtm180) cc_final: 0.7242 (mmp-170) REVERT: E 136 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 142 MET cc_start: 0.9171 (tpp) cc_final: 0.8756 (tpt) REVERT: F 6 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7432 (mm-30) REVERT: F 7 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7366 (mmp-170) REVERT: F 24 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6949 (tm-30) REVERT: F 47 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7311 (ttmt) REVERT: F 136 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7754 (tm-30) REVERT: F 169 GLU cc_start: 0.8402 (tp30) cc_final: 0.8193 (tt0) REVERT: G 6 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8082 (mm-30) REVERT: G 7 ARG cc_start: 0.7451 (mtm180) cc_final: 0.7100 (mmp-170) REVERT: G 136 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7875 (tm-30) REVERT: G 192 ILE cc_start: 0.8693 (tt) cc_final: 0.8355 (tt) REVERT: H 7 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7449 (mpt180) REVERT: H 136 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7742 (tm-30) REVERT: H 142 MET cc_start: 0.9137 (tpp) cc_final: 0.8579 (tpt) REVERT: H 169 GLU cc_start: 0.8295 (tp30) cc_final: 0.8077 (tt0) REVERT: H 192 ILE cc_start: 0.8858 (tt) cc_final: 0.8529 (tt) outliers start: 26 outliers final: 9 residues processed: 223 average time/residue: 0.2455 time to fit residues: 77.8903 Evaluate side-chains 162 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN G 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12528 Z= 0.259 Angle : 0.535 6.960 16888 Z= 0.280 Chirality : 0.032 0.177 1936 Planarity : 0.003 0.026 2152 Dihedral : 3.348 11.976 1688 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.21 % Allowed : 11.15 % Favored : 85.64 % 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: 3.47 (0.20), residues: 1576 helix: 2.58 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.97 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 113 PHE 0.011 0.001 PHE G 183 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 1.500 Fit side-chains REVERT: A 7 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7365 (mmp-170) REVERT: A 47 LYS cc_start: 0.7621 (mmtm) cc_final: 0.7209 (ttmt) REVERT: A 136 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7909 (tm-30) REVERT: B 6 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7484 (mm-30) REVERT: B 7 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7220 (mmp-170) REVERT: B 24 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6988 (tm-30) REVERT: B 47 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7231 (ttmm) REVERT: B 132 GLU cc_start: 0.7824 (tp30) cc_final: 0.7601 (tp30) REVERT: B 136 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 136 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7897 (tm-30) REVERT: C 142 MET cc_start: 0.9108 (tpp) cc_final: 0.8728 (tpt) REVERT: D 7 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7516 (mpt180) REVERT: D 47 LYS cc_start: 0.7796 (mmtm) cc_final: 0.6931 (ttmt) REVERT: D 50 ASP cc_start: 0.8115 (t0) cc_final: 0.7905 (t0) REVERT: D 136 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 142 MET cc_start: 0.9004 (tpp) cc_final: 0.8497 (tpt) REVERT: E 6 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8039 (mm-30) REVERT: E 7 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7361 (mmp-170) REVERT: E 47 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7302 (ttmt) REVERT: E 136 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 142 MET cc_start: 0.9183 (tpp) cc_final: 0.8736 (tpt) REVERT: F 6 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7431 (mm-30) REVERT: F 7 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7344 (mmp-170) REVERT: F 47 LYS cc_start: 0.7794 (mmtm) cc_final: 0.7168 (ttmt) REVERT: F 136 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7787 (tm-30) REVERT: F 169 GLU cc_start: 0.8409 (tp30) cc_final: 0.8157 (tt0) REVERT: G 6 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8064 (mm-30) REVERT: G 7 ARG cc_start: 0.7507 (mtm180) cc_final: 0.7147 (mmp-170) REVERT: G 47 LYS cc_start: 0.7734 (mmtm) cc_final: 0.7156 (ttmm) REVERT: G 136 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7892 (tm-30) REVERT: H 7 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7508 (mpt180) REVERT: H 47 LYS cc_start: 0.7708 (mmtm) cc_final: 0.6787 (ttmm) REVERT: H 136 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7711 (tm-30) REVERT: H 142 MET cc_start: 0.9149 (tpp) cc_final: 0.8460 (tpt) REVERT: H 155 GLU cc_start: 0.7926 (tt0) cc_final: 0.7658 (tt0) outliers start: 38 outliers final: 14 residues processed: 224 average time/residue: 0.2351 time to fit residues: 75.9932 Evaluate side-chains 163 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 0.0070 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12528 Z= 0.219 Angle : 0.483 7.268 16888 Z= 0.257 Chirality : 0.031 0.111 1936 Planarity : 0.003 0.023 2152 Dihedral : 3.304 12.253 1688 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.36 % Allowed : 14.19 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.20), residues: 1576 helix: 2.81 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.45 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 113 PHE 0.010 0.001 PHE C 27 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.468 Fit side-chains REVERT: A 47 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7381 (pttt) REVERT: A 136 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 6 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 7 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7221 (mmp-170) REVERT: B 47 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7295 (ttmt) REVERT: B 136 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 136 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7883 (tm-30) REVERT: D 7 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7514 (mpt180) REVERT: D 47 LYS cc_start: 0.7809 (mmtm) cc_final: 0.6880 (ttmm) REVERT: D 50 ASP cc_start: 0.8150 (t0) cc_final: 0.7934 (t0) REVERT: D 136 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7742 (tm-30) REVERT: D 146 MET cc_start: 0.8261 (tmm) cc_final: 0.7932 (tmm) REVERT: E 6 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8006 (mm-30) REVERT: E 7 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7412 (mmp-170) REVERT: E 47 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7227 (ttmt) REVERT: E 136 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7896 (tm-30) REVERT: E 142 MET cc_start: 0.9189 (tpp) cc_final: 0.8891 (tpt) REVERT: F 7 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7375 (mmp-170) REVERT: F 47 LYS cc_start: 0.7757 (mmtm) cc_final: 0.7137 (ttmt) REVERT: F 136 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7761 (tm-30) REVERT: F 146 MET cc_start: 0.8155 (tmm) cc_final: 0.7948 (tmm) REVERT: G 6 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8030 (mm-30) REVERT: G 7 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7206 (mmp-170) REVERT: G 47 LYS cc_start: 0.7653 (mmtm) cc_final: 0.7158 (ttmm) REVERT: G 136 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7945 (tm-30) REVERT: G 155 GLU cc_start: 0.7774 (tt0) cc_final: 0.7548 (tt0) REVERT: H 7 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7492 (mpt180) REVERT: H 47 LYS cc_start: 0.7788 (mmtm) cc_final: 0.7055 (ttmt) REVERT: H 82 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7926 (mm-30) REVERT: H 136 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7695 (tm-30) REVERT: H 142 MET cc_start: 0.9262 (tpp) cc_final: 0.8996 (tpt) REVERT: H 146 MET cc_start: 0.8253 (tmm) cc_final: 0.7935 (tmm) REVERT: H 155 GLU cc_start: 0.7923 (tt0) cc_final: 0.7632 (tt0) outliers start: 28 outliers final: 17 residues processed: 218 average time/residue: 0.2398 time to fit residues: 75.6921 Evaluate side-chains 176 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12528 Z= 0.175 Angle : 0.470 9.252 16888 Z= 0.247 Chirality : 0.030 0.165 1936 Planarity : 0.002 0.021 2152 Dihedral : 3.222 11.845 1688 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.36 % Allowed : 16.39 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.20), residues: 1576 helix: 2.97 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.29 (0.64), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 113 PHE 0.018 0.001 PHE E 27 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 1.445 Fit side-chains REVERT: A 47 LYS cc_start: 0.7595 (mmtm) cc_final: 0.7385 (pttt) REVERT: A 136 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 6 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 7 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7167 (mmp-170) REVERT: B 47 LYS cc_start: 0.7864 (mmtm) cc_final: 0.7335 (ttmt) REVERT: B 73 ASP cc_start: 0.7908 (t70) cc_final: 0.7700 (t70) REVERT: B 136 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7820 (tm-30) REVERT: C 47 LYS cc_start: 0.7691 (mmtm) cc_final: 0.7112 (pttt) REVERT: C 136 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7789 (tm-30) REVERT: D 7 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7500 (mpt180) REVERT: D 47 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7023 (ttmt) REVERT: D 67 LEU cc_start: 0.9179 (mm) cc_final: 0.8808 (mm) REVERT: D 136 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7677 (tm-30) REVERT: E 7 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7416 (mmp-170) REVERT: E 47 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7354 (pttt) REVERT: E 136 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7920 (tm-30) REVERT: F 7 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7368 (mmp-170) REVERT: F 35 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8534 (mm) REVERT: F 47 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7104 (ttmm) REVERT: F 136 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7824 (tm-30) REVERT: G 6 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8016 (mm-30) REVERT: G 7 ARG cc_start: 0.7622 (mtm180) cc_final: 0.7279 (mmp-170) REVERT: G 47 LYS cc_start: 0.7586 (mmtm) cc_final: 0.7141 (ttmm) REVERT: G 136 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7852 (tm-30) REVERT: H 7 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7551 (mpt180) REVERT: H 47 LYS cc_start: 0.7761 (mmtm) cc_final: 0.7024 (ttmm) REVERT: H 67 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8842 (mm) REVERT: H 82 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7849 (mm-30) REVERT: H 136 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7649 (tm-30) REVERT: H 142 MET cc_start: 0.9310 (tpp) cc_final: 0.9070 (tpt) REVERT: H 155 GLU cc_start: 0.7861 (tt0) cc_final: 0.7633 (tt0) REVERT: H 192 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8460 (tp) outliers start: 28 outliers final: 14 residues processed: 235 average time/residue: 0.2346 time to fit residues: 79.3839 Evaluate side-chains 194 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 192 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8091 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12528 Z= 0.184 Angle : 0.487 7.929 16888 Z= 0.254 Chirality : 0.031 0.124 1936 Planarity : 0.002 0.020 2152 Dihedral : 3.204 12.256 1688 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.63 % Allowed : 16.05 % Favored : 80.32 % 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: 4.21 (0.20), residues: 1576 helix: 3.01 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.32 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 113 PHE 0.022 0.001 PHE F 27 ARG 0.002 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7370 (pttt) REVERT: A 136 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 6 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7484 (mm-30) REVERT: B 7 ARG cc_start: 0.7640 (mtm180) cc_final: 0.7167 (mmp-170) REVERT: B 47 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7133 (ttmm) REVERT: B 136 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 143 GLU cc_start: 0.8299 (tp30) cc_final: 0.7976 (tm-30) REVERT: C 47 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7135 (pttt) REVERT: C 136 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7770 (tm-30) REVERT: D 7 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7493 (mpt180) REVERT: D 47 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7062 (ttmt) REVERT: D 67 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8900 (mm) REVERT: D 73 ASP cc_start: 0.8168 (t70) cc_final: 0.7821 (t70) REVERT: D 136 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 7 ARG cc_start: 0.7690 (mtm180) cc_final: 0.7438 (mmp-170) REVERT: E 47 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7415 (pttt) REVERT: E 136 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7908 (tm-30) REVERT: E 142 MET cc_start: 0.9213 (tpp) cc_final: 0.8867 (mmm) REVERT: F 7 ARG cc_start: 0.7817 (mtm180) cc_final: 0.7423 (mpt180) REVERT: F 35 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8530 (mm) REVERT: F 47 LYS cc_start: 0.7791 (mmtm) cc_final: 0.7207 (ttmt) REVERT: F 67 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8886 (mm) REVERT: F 73 ASP cc_start: 0.7767 (t70) cc_final: 0.7463 (t70) REVERT: F 136 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7811 (tm-30) REVERT: G 6 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7990 (mm-30) REVERT: G 7 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7334 (mmp-170) REVERT: G 136 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7811 (tm-30) REVERT: H 7 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7556 (mpt180) REVERT: H 47 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7086 (ttmt) REVERT: H 67 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8852 (mm) REVERT: H 82 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7796 (mm-30) REVERT: H 136 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7656 (tm-30) REVERT: H 155 GLU cc_start: 0.7957 (tt0) cc_final: 0.7675 (tt0) outliers start: 43 outliers final: 17 residues processed: 233 average time/residue: 0.2235 time to fit residues: 76.2279 Evaluate side-chains 192 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12528 Z= 0.181 Angle : 0.499 7.373 16888 Z= 0.261 Chirality : 0.033 0.253 1936 Planarity : 0.002 0.018 2152 Dihedral : 3.234 12.106 1688 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.36 % Allowed : 18.07 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.20), residues: 1576 helix: 3.04 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : -1.62 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 197 PHE 0.022 0.001 PHE B 27 ARG 0.002 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.396 Fit side-chains REVERT: A 47 LYS cc_start: 0.7586 (mmtm) cc_final: 0.7349 (pttt) REVERT: A 136 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 6 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 7 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7190 (mmp-170) REVERT: B 47 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7169 (ttmm) REVERT: B 67 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8869 (mm) REVERT: B 136 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 143 GLU cc_start: 0.8302 (tp30) cc_final: 0.7982 (tm-30) REVERT: C 47 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7167 (pttt) REVERT: C 136 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7825 (tm-30) REVERT: D 7 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7520 (mpt180) REVERT: D 47 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7101 (ttmt) REVERT: D 67 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8967 (mm) REVERT: D 136 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 7 ARG cc_start: 0.7757 (mtm180) cc_final: 0.7465 (mmp-170) REVERT: E 47 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7402 (pttt) REVERT: E 136 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7891 (tm-30) REVERT: F 7 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7424 (mpt180) REVERT: F 47 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7088 (ttmm) REVERT: F 67 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8886 (mm) REVERT: F 136 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7809 (tm-30) REVERT: G 7 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7415 (mmp-170) REVERT: G 47 LYS cc_start: 0.7582 (mmtm) cc_final: 0.7360 (pttt) REVERT: G 136 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7764 (tm-30) REVERT: H 7 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7530 (mpt180) REVERT: H 47 LYS cc_start: 0.7723 (mmtm) cc_final: 0.7080 (ttmt) REVERT: H 67 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8868 (mm) REVERT: H 82 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7786 (mm-30) REVERT: H 136 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7665 (tm-30) REVERT: H 155 GLU cc_start: 0.7873 (tt0) cc_final: 0.7635 (tt0) outliers start: 28 outliers final: 19 residues processed: 215 average time/residue: 0.2304 time to fit residues: 72.3600 Evaluate side-chains 185 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN F 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12528 Z= 0.250 Angle : 0.553 8.286 16888 Z= 0.287 Chirality : 0.035 0.302 1936 Planarity : 0.003 0.021 2152 Dihedral : 3.272 12.852 1688 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.36 % Allowed : 18.16 % 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: 4.11 (0.20), residues: 1576 helix: 2.98 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : -1.65 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 197 PHE 0.023 0.002 PHE F 27 ARG 0.002 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8325 (t0) cc_final: 0.8091 (t0) REVERT: A 136 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 6 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 7 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7238 (mmp-170) REVERT: B 47 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7245 (ttmt) REVERT: B 67 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8891 (mm) REVERT: B 136 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 143 GLU cc_start: 0.8330 (tp30) cc_final: 0.8035 (tm-30) REVERT: C 10 GLU cc_start: 0.6820 (tp30) cc_final: 0.6463 (tm-30) REVERT: C 121 ASN cc_start: 0.8364 (t0) cc_final: 0.8132 (t0) REVERT: C 136 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 143 GLU cc_start: 0.8182 (tp30) cc_final: 0.7781 (tm-30) REVERT: D 7 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7513 (mpt180) REVERT: D 136 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7811 (tm-30) REVERT: E 7 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7500 (mmp-170) REVERT: E 136 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7924 (tm-30) REVERT: F 7 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7413 (mpt180) REVERT: F 67 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8887 (mm) REVERT: F 136 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7832 (tm-30) REVERT: G 7 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7324 (mmp-170) REVERT: G 47 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7331 (pttt) REVERT: G 121 ASN cc_start: 0.8313 (t0) cc_final: 0.8080 (t0) REVERT: G 136 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7885 (tm-30) REVERT: H 7 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7445 (mpt180) REVERT: H 47 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7076 (ttmt) REVERT: H 67 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8876 (mm) REVERT: H 136 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7784 (tm-30) REVERT: H 155 GLU cc_start: 0.7947 (tt0) cc_final: 0.7701 (tt0) outliers start: 28 outliers final: 20 residues processed: 192 average time/residue: 0.2422 time to fit residues: 66.8583 Evaluate side-chains 179 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12528 Z= 0.216 Angle : 0.538 9.514 16888 Z= 0.280 Chirality : 0.035 0.293 1936 Planarity : 0.003 0.022 2152 Dihedral : 3.291 12.391 1688 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.03 % Allowed : 18.16 % Favored : 79.81 % 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: 4.05 (0.20), residues: 1576 helix: 2.94 (0.12), residues: 1464 sheet: None (None), residues: 0 loop : -1.54 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 197 PHE 0.023 0.001 PHE B 27 ARG 0.004 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.530 Fit side-chains REVERT: A 47 LYS cc_start: 0.7625 (mmtm) cc_final: 0.7281 (pttt) REVERT: A 121 ASN cc_start: 0.8270 (t0) cc_final: 0.8035 (t0) REVERT: A 136 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 6 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 7 ARG cc_start: 0.7701 (mtm180) cc_final: 0.7227 (mmp-170) REVERT: B 47 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7260 (ttmt) REVERT: B 67 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8886 (mm) REVERT: B 136 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 143 GLU cc_start: 0.8298 (tp30) cc_final: 0.8062 (tm-30) REVERT: C 10 GLU cc_start: 0.6907 (tp30) cc_final: 0.6440 (tm-30) REVERT: C 121 ASN cc_start: 0.8319 (t0) cc_final: 0.8077 (t0) REVERT: C 136 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 143 GLU cc_start: 0.8174 (tp30) cc_final: 0.7760 (tm-30) REVERT: D 7 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7434 (mpt180) REVERT: D 47 LYS cc_start: 0.7527 (mmtm) cc_final: 0.6857 (ttmt) REVERT: D 136 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7796 (tm-30) REVERT: E 7 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7473 (mmp-170) REVERT: E 47 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7352 (pttt) REVERT: E 136 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7895 (tm-30) REVERT: F 7 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7434 (mpt180) REVERT: F 47 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7037 (ttmm) REVERT: F 67 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8895 (mm) REVERT: F 136 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7831 (tm-30) REVERT: G 7 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7370 (mmp-170) REVERT: G 47 LYS cc_start: 0.7631 (mmtm) cc_final: 0.7285 (pttt) REVERT: G 121 ASN cc_start: 0.8257 (t0) cc_final: 0.8007 (t0) REVERT: G 136 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7881 (tm-30) REVERT: H 7 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7434 (mpt180) REVERT: H 47 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7000 (ttmm) REVERT: H 67 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8871 (mm) REVERT: H 136 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7823 (tm-30) REVERT: H 155 GLU cc_start: 0.7814 (tt0) cc_final: 0.7597 (tt0) outliers start: 24 outliers final: 19 residues processed: 186 average time/residue: 0.2435 time to fit residues: 66.8528 Evaluate side-chains 176 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN F 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12528 Z= 0.205 Angle : 0.548 14.493 16888 Z= 0.282 Chirality : 0.034 0.305 1936 Planarity : 0.002 0.021 2152 Dihedral : 3.278 12.555 1688 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.20 % Allowed : 18.33 % 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: 4.08 (0.20), residues: 1576 helix: 2.92 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.26 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 197 PHE 0.024 0.001 PHE B 27 ARG 0.004 0.000 ARG E 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.452 Fit side-chains REVERT: A 27 PHE cc_start: 0.7187 (t80) cc_final: 0.6950 (t80) REVERT: A 47 LYS cc_start: 0.7691 (mmtm) cc_final: 0.7399 (pttt) REVERT: A 121 ASN cc_start: 0.8282 (t0) cc_final: 0.8041 (t0) REVERT: A 136 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 6 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 7 ARG cc_start: 0.7694 (mtm180) cc_final: 0.7235 (mmp-170) REVERT: B 47 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7126 (ttmm) REVERT: B 67 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8890 (mm) REVERT: B 136 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 143 GLU cc_start: 0.8318 (tp30) cc_final: 0.8012 (tm-30) REVERT: C 10 GLU cc_start: 0.6915 (tp30) cc_final: 0.6451 (tm-30) REVERT: C 121 ASN cc_start: 0.8312 (t0) cc_final: 0.8068 (t0) REVERT: C 136 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 143 GLU cc_start: 0.8175 (tp30) cc_final: 0.7749 (tm-30) REVERT: D 7 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7542 (mpt180) REVERT: D 47 LYS cc_start: 0.7511 (mmtm) cc_final: 0.6823 (ttmt) REVERT: D 136 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7781 (tm-30) REVERT: E 7 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7492 (mmp-170) REVERT: E 47 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7203 (ttmt) REVERT: E 136 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7906 (tm-30) REVERT: F 7 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7439 (mpt180) REVERT: F 47 LYS cc_start: 0.7766 (mmtm) cc_final: 0.7033 (ttmm) REVERT: F 67 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8908 (mm) REVERT: F 136 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7849 (tm-30) REVERT: G 7 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7308 (mmp-170) REVERT: G 10 GLU cc_start: 0.6876 (tp30) cc_final: 0.6370 (tm-30) REVERT: G 47 LYS cc_start: 0.7623 (mmtm) cc_final: 0.7284 (pttt) REVERT: G 121 ASN cc_start: 0.8243 (t0) cc_final: 0.7988 (t0) REVERT: G 136 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7869 (tm-30) REVERT: H 7 ARG cc_start: 0.7738 (mtm180) cc_final: 0.7432 (mpt180) REVERT: H 47 LYS cc_start: 0.7787 (mmtm) cc_final: 0.6992 (ttmm) REVERT: H 67 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8865 (mm) REVERT: H 136 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7841 (tm-30) REVERT: H 143 GLU cc_start: 0.8323 (tp30) cc_final: 0.7951 (tm-30) REVERT: H 155 GLU cc_start: 0.7816 (tt0) cc_final: 0.7610 (tt0) outliers start: 26 outliers final: 21 residues processed: 195 average time/residue: 0.2416 time to fit residues: 68.1787 Evaluate side-chains 177 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.140246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094868 restraints weight = 19536.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097788 restraints weight = 11472.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099733 restraints weight = 8265.897| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12528 Z= 0.187 Angle : 0.527 10.145 16888 Z= 0.277 Chirality : 0.033 0.326 1936 Planarity : 0.002 0.019 2152 Dihedral : 3.265 12.300 1688 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.86 % Allowed : 18.92 % Favored : 79.22 % 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: 4.17 (0.20), residues: 1576 helix: 2.97 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.25 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 113 PHE 0.024 0.001 PHE F 27 ARG 0.004 0.000 ARG E 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.32 seconds wall clock time: 41 minutes 42.62 seconds (2502.62 seconds total)