Starting phenix.real_space_refine on Fri Dec 8 02:52:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/12_2023/8d1b_27121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/12_2023/8d1b_27121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/12_2023/8d1b_27121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/12_2023/8d1b_27121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/12_2023/8d1b_27121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/12_2023/8d1b_27121.pdb" } resolution = 3.57 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4196 2.51 5 N 1204 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 861": "NH1" <-> "NH2" Residue "D ARG 867": "NH1" <-> "NH2" Residue "D PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 924": "NH1" <-> "NH2" Residue "D ARG 927": "NH1" <-> "NH2" Residue "D ASP 933": "OD1" <-> "OD2" Residue "D ASP 942": "OD1" <-> "OD2" Residue "D TYR 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 971": "OE1" <-> "OE2" Residue "C ARG 861": "NH1" <-> "NH2" Residue "C ARG 867": "NH1" <-> "NH2" Residue "C PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 924": "NH1" <-> "NH2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C ASP 933": "OD1" <-> "OD2" Residue "C ASP 942": "OD1" <-> "OD2" Residue "C TYR 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6724 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1379 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "C" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1379 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "B" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1983 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Chain: "A" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1983 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Time building chain proxies: 3.96, per 1000 atoms: 0.59 Number of scatterers: 6724 At special positions: 0 Unit cell: (86.355, 88.065, 112.005, 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 38 16.00 O 1286 8.00 N 1204 7.00 C 4196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 987 " - pdb=" SG CYS D1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS C1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 317 " distance=2.03 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: 2.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 10.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'D' and resid 852 through 857 removed outlier: 4.190A pdb=" N VAL D 857 " --> pdb=" O ILE D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 996 removed outlier: 3.983A pdb=" N THR D 995 " --> pdb=" O THR D 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 removed outlier: 4.190A pdb=" N VAL C 857 " --> pdb=" O ILE C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 996 removed outlier: 3.983A pdb=" N THR C 995 " --> pdb=" O THR C 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 removed outlier: 3.788A pdb=" N ALA B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.660A pdb=" N GLN B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.720A pdb=" N ALA B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.787A pdb=" N ALA A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.659A pdb=" N GLN A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.720A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 136 through 140 Processing sheet with id=AA1, first strand: chain 'D' and resid 894 through 897 removed outlier: 3.562A pdb=" N GLY D 895 " --> pdb=" O VAL D 902 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 894 through 897 removed outlier: 3.562A pdb=" N GLY C 895 " --> pdb=" O VAL C 902 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.590A pdb=" N ASP B 271 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 146 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 149 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR B 173 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 219 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 216 through 221 removed outlier: 3.671A pdb=" N GLY B 219 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 173 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 149 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 146 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP A 271 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.718A pdb=" N GLN B 237 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237 removed outlier: 3.717A pdb=" N GLN A 237 " --> pdb=" O ARG A 240 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 162 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: 1.45 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2301 1.34 - 1.46: 1523 1.46 - 1.58: 2976 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6858 Sorted by residual: bond pdb=" C GLN A 114 " pdb=" N ALA A 115 " ideal model delta sigma weight residual 1.331 1.306 0.025 1.73e-02 3.34e+03 2.10e+00 bond pdb=" C GLN B 114 " pdb=" N ALA B 115 " ideal model delta sigma weight residual 1.331 1.306 0.025 1.73e-02 3.34e+03 2.02e+00 bond pdb=" C ALA B 106 " pdb=" N ASN B 107 " ideal model delta sigma weight residual 1.331 1.311 0.019 1.38e-02 5.25e+03 1.97e+00 bond pdb=" C ALA A 106 " pdb=" N ASN A 107 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.38e-02 5.25e+03 1.68e+00 bond pdb=" CB VAL A 134 " pdb=" CG1 VAL A 134 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 ... (remaining 6853 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.87: 182 105.87 - 112.91: 3515 112.91 - 119.94: 2348 119.94 - 126.98: 3171 126.98 - 134.01: 78 Bond angle restraints: 9294 Sorted by residual: angle pdb=" N GLY B 86 " pdb=" CA GLY B 86 " pdb=" C GLY B 86 " ideal model delta sigma weight residual 113.99 108.54 5.45 1.28e+00 6.10e-01 1.81e+01 angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 113.99 108.55 5.44 1.28e+00 6.10e-01 1.81e+01 angle pdb=" N LYS B 257 " pdb=" CA LYS B 257 " pdb=" C LYS B 257 " ideal model delta sigma weight residual 109.83 104.83 5.00 1.27e+00 6.20e-01 1.55e+01 angle pdb=" N LYS A 257 " pdb=" CA LYS A 257 " pdb=" C LYS A 257 " ideal model delta sigma weight residual 109.83 104.88 4.95 1.27e+00 6.20e-01 1.52e+01 angle pdb=" CA LEU B 71 " pdb=" C LEU B 71 " pdb=" N SER B 72 " ideal model delta sigma weight residual 114.17 119.36 -5.19 1.45e+00 4.76e-01 1.28e+01 ... (remaining 9289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3664 17.78 - 35.56: 390 35.56 - 53.34: 64 53.34 - 71.13: 6 71.13 - 88.91: 4 Dihedral angle restraints: 4128 sinusoidal: 1656 harmonic: 2472 Sorted by residual: dihedral pdb=" CA ARG C 886 " pdb=" C ARG C 886 " pdb=" N PRO C 887 " pdb=" CA PRO C 887 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG D 886 " pdb=" C ARG D 886 " pdb=" N PRO D 887 " pdb=" CA PRO D 887 " ideal model delta harmonic sigma weight residual 180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N VAL A 264 " pdb=" CA VAL A 264 " ideal model delta harmonic sigma weight residual 180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 4125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 550 0.037 - 0.073: 308 0.073 - 0.109: 119 0.109 - 0.146: 23 0.146 - 0.182: 10 Chirality restraints: 1010 Sorted by residual: chirality pdb=" CA PRO D 887 " pdb=" N PRO D 887 " pdb=" C PRO D 887 " pdb=" CB PRO D 887 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA PRO C 887 " pdb=" N PRO C 887 " pdb=" C PRO C 887 " pdb=" CB PRO C 887 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CB THR B 173 " pdb=" CA THR B 173 " pdb=" OG1 THR B 173 " pdb=" CG2 THR B 173 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1007 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 93 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 92 " 0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 93 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 257 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO B 258 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.039 5.00e-02 4.00e+02 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 168 2.65 - 3.21: 6399 3.21 - 3.77: 9281 3.77 - 4.34: 12952 4.34 - 4.90: 21299 Nonbonded interactions: 50099 Sorted by model distance: nonbonded pdb=" OE1 GLN B 73 " pdb=" NH2 ARG B 240 " model vdw 2.084 2.520 nonbonded pdb=" OE1 GLN A 73 " pdb=" NH2 ARG A 240 " model vdw 2.085 2.520 nonbonded pdb=" NZ LYS C 950 " pdb=" OD1 ASP A 259 " model vdw 2.105 2.520 nonbonded pdb=" O SER B 261 " pdb=" OG SER B 261 " model vdw 2.112 2.440 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 261 " model vdw 2.112 2.440 ... (remaining 50094 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.170 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: 0.000 Extract box with map and model: 22.270 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.350 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.042 6858 Z= 0.405 Angle : 1.086 9.237 9294 Z= 0.620 Chirality : 0.052 0.182 1010 Planarity : 0.008 0.084 1232 Dihedral : 14.425 88.908 2532 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.13 % Favored : 75.87 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.45 % 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: -6.32 (0.22), residues: 862 helix: -5.21 (0.17), residues: 100 sheet: -3.30 (0.35), residues: 164 loop : -4.63 (0.20), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 182 HIS 0.003 0.001 HIS D 926 PHE 0.013 0.002 PHE D 868 TYR 0.023 0.002 TYR A 62 ARG 0.005 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.770 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.1437 time to fit residues: 26.6733 Evaluate side-chains 100 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS B 161 GLN B 165 GLN B 237 GLN A 161 GLN A 165 GLN A 237 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6858 Z= 0.237 Angle : 0.809 8.562 9294 Z= 0.410 Chirality : 0.047 0.186 1010 Planarity : 0.006 0.068 1232 Dihedral : 6.978 27.131 958 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.84 % Favored : 80.16 % Rotamer: Outliers : 0.97 % Allowed : 10.11 % Favored : 88.92 % 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: -5.80 (0.23), residues: 862 helix: -4.77 (0.26), residues: 90 sheet: -2.73 (0.39), residues: 160 loop : -4.38 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.006 0.001 HIS D 990 PHE 0.008 0.001 PHE D 868 TYR 0.021 0.002 TYR A 62 ARG 0.004 0.001 ARG D 886 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.784 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 122 average time/residue: 0.1461 time to fit residues: 25.6805 Evaluate side-chains 105 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0719 time to fit residues: 1.2743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1010 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6858 Z= 0.226 Angle : 0.773 7.863 9294 Z= 0.388 Chirality : 0.046 0.184 1010 Planarity : 0.006 0.065 1232 Dihedral : 6.502 27.849 958 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.56 % Favored : 81.44 % Rotamer: Outliers : 0.55 % Allowed : 15.65 % Favored : 83.80 % 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: -5.69 (0.23), residues: 862 helix: -4.39 (0.32), residues: 90 sheet: -2.69 (0.37), residues: 164 loop : -4.35 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.001 0.000 HIS D 998 PHE 0.007 0.001 PHE D 868 TYR 0.015 0.001 TYR B 80 ARG 0.003 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.754 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 106 average time/residue: 0.1481 time to fit residues: 22.5301 Evaluate side-chains 98 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 839 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6858 Z= 0.249 Angle : 0.767 7.859 9294 Z= 0.381 Chirality : 0.046 0.192 1010 Planarity : 0.005 0.064 1232 Dihedral : 6.216 27.951 958 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.79 % Favored : 81.21 % Rotamer: Outliers : 2.49 % Allowed : 17.31 % Favored : 80.19 % 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: -5.54 (0.23), residues: 862 helix: -4.27 (0.31), residues: 90 sheet: -2.49 (0.38), residues: 164 loop : -4.28 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 245 HIS 0.002 0.001 HIS C 926 PHE 0.008 0.001 PHE D 868 TYR 0.012 0.001 TYR B 80 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.694 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 118 average time/residue: 0.1451 time to fit residues: 24.8361 Evaluate side-chains 100 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0606 time to fit residues: 1.3847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.0030 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 overall best weight: 0.5430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1012 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6858 Z= 0.217 Angle : 0.748 9.316 9294 Z= 0.369 Chirality : 0.045 0.185 1010 Planarity : 0.005 0.063 1232 Dihedral : 6.012 27.263 958 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.47 % Favored : 83.53 % Rotamer: Outliers : 1.25 % Allowed : 18.98 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.30 (0.24), residues: 862 helix: -4.09 (0.34), residues: 88 sheet: -2.28 (0.39), residues: 164 loop : -4.13 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 245 HIS 0.001 0.000 HIS C 926 PHE 0.009 0.001 PHE A 253 TYR 0.008 0.001 TYR B 62 ARG 0.004 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.802 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 112 average time/residue: 0.1501 time to fit residues: 24.4788 Evaluate side-chains 99 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0662 time to fit residues: 1.2656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 0.0010 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.0270 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 overall best weight: 0.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6858 Z= 0.182 Angle : 0.728 10.281 9294 Z= 0.355 Chirality : 0.044 0.185 1010 Planarity : 0.005 0.061 1232 Dihedral : 5.619 26.969 958 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer: Outliers : 0.83 % Allowed : 20.36 % Favored : 78.81 % 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: -5.07 (0.24), residues: 862 helix: -3.83 (0.37), residues: 96 sheet: -2.20 (0.38), residues: 168 loop : -3.95 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 288 HIS 0.002 0.000 HIS C 975 PHE 0.010 0.001 PHE B 253 TYR 0.011 0.001 TYR A 80 ARG 0.002 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.768 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 108 average time/residue: 0.1593 time to fit residues: 24.3007 Evaluate side-chains 108 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0646 time to fit residues: 1.5321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 0.0050 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.0370 overall best weight: 0.1748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6858 Z= 0.175 Angle : 0.686 11.090 9294 Z= 0.338 Chirality : 0.043 0.184 1010 Planarity : 0.005 0.059 1232 Dihedral : 5.382 26.119 958 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer: Outliers : 1.39 % Allowed : 21.05 % Favored : 77.56 % 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: -4.88 (0.25), residues: 862 helix: -3.63 (0.39), residues: 96 sheet: -1.99 (0.38), residues: 168 loop : -3.85 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 245 HIS 0.002 0.000 HIS D 975 PHE 0.008 0.001 PHE D 840 TYR 0.006 0.001 TYR B 254 ARG 0.002 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.747 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 111 average time/residue: 0.1638 time to fit residues: 25.3370 Evaluate side-chains 99 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0679 time to fit residues: 1.5138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6858 Z= 0.215 Angle : 0.733 11.255 9294 Z= 0.358 Chirality : 0.043 0.184 1010 Planarity : 0.005 0.059 1232 Dihedral : 5.389 25.973 958 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.63 % Favored : 82.37 % Rotamer: Outliers : 1.11 % Allowed : 20.64 % Favored : 78.25 % 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: -4.78 (0.25), residues: 862 helix: -3.57 (0.40), residues: 96 sheet: -1.92 (0.38), residues: 168 loop : -3.78 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 879 HIS 0.002 0.001 HIS D 975 PHE 0.008 0.001 PHE D 840 TYR 0.010 0.001 TYR B 80 ARG 0.002 0.000 ARG D 932 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.767 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 0.1571 time to fit residues: 22.0808 Evaluate side-chains 94 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0740 time to fit residues: 1.4310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7743 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6858 Z= 0.279 Angle : 0.778 11.470 9294 Z= 0.383 Chirality : 0.045 0.184 1010 Planarity : 0.005 0.059 1232 Dihedral : 5.581 26.014 958 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.79 % Favored : 81.21 % Rotamer: Outliers : 1.25 % Allowed : 20.50 % Favored : 78.25 % 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: -4.76 (0.25), residues: 862 helix: -3.48 (0.42), residues: 88 sheet: -1.96 (0.38), residues: 164 loop : -3.77 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 879 HIS 0.002 0.001 HIS C 975 PHE 0.007 0.001 PHE C 865 TYR 0.015 0.001 TYR A 80 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.639 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 108 average time/residue: 0.1765 time to fit residues: 26.2706 Evaluate side-chains 98 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0663 time to fit residues: 1.2957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.0010 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS B 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6858 Z= 0.236 Angle : 0.757 11.380 9294 Z= 0.372 Chirality : 0.045 0.191 1010 Planarity : 0.005 0.058 1232 Dihedral : 5.572 25.952 958 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.45 % Favored : 81.55 % Rotamer: Outliers : 0.69 % Allowed : 21.47 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.25), residues: 862 helix: -3.66 (0.39), residues: 96 sheet: -1.96 (0.39), residues: 164 loop : -3.76 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 879 HIS 0.002 0.001 HIS D 975 PHE 0.008 0.001 PHE D 840 TYR 0.012 0.001 TYR A 80 ARG 0.002 0.000 ARG B 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.808 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 99 average time/residue: 0.1589 time to fit residues: 22.6620 Evaluate side-chains 93 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0654 time to fit residues: 1.1016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.157332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126419 restraints weight = 10206.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130360 restraints weight = 5963.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132916 restraints weight = 4297.292| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6858 Z= 0.225 Angle : 0.774 14.456 9294 Z= 0.374 Chirality : 0.044 0.184 1010 Planarity : 0.005 0.058 1232 Dihedral : 5.486 26.494 958 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.52 % Favored : 82.48 % Rotamer: Outliers : 0.55 % Allowed : 22.30 % Favored : 77.15 % 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: -4.80 (0.26), residues: 862 helix: -3.61 (0.40), residues: 96 sheet: -2.27 (0.36), residues: 192 loop : -3.70 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 879 HIS 0.002 0.001 HIS D 975 PHE 0.011 0.001 PHE D 865 TYR 0.011 0.001 TYR A 80 ARG 0.003 0.000 ARG D 867 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.57 seconds wall clock time: 38 minutes 16.84 seconds (2296.84 seconds total)