Starting phenix.real_space_refine on Thu Feb 15 22:48:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk3_25171/02_2024/7sk3_25171_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk3_25171/02_2024/7sk3_25171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk3_25171/02_2024/7sk3_25171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk3_25171/02_2024/7sk3_25171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk3_25171/02_2024/7sk3_25171_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk3_25171/02_2024/7sk3_25171_trim_updated.pdb" } resolution = 3.8 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= -0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 4480 2.51 5 N 1079 2.21 5 O 1206 1.98 5 H 6491 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13294 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4967 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1145 Classifications: {'peptide': 68} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "C" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1592 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1888 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1607 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1871 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 224 Unusual residues: {'CLR': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 5.96, per 1000 atoms: 0.45 Number of scatterers: 13294 At special positions: 0 Unit cell: (70.2, 71.28, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1206 8.00 N 1079 7.00 C 4480 6.00 H 6491 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " 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: 9.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 11 sheets defined 30.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 41 through 75 removed outlier: 3.824A pdb=" N ALA A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 105 removed outlier: 3.710A pdb=" N THR A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.939A pdb=" N SER A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 154 through 181 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 205 through 218 removed outlier: 4.272A pdb=" N SER A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.590A pdb=" N LYS A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 252 through 280 removed outlier: 3.891A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.575A pdb=" N LEU A 273 " --> pdb=" O HIS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 308 removed outlier: 4.099A pdb=" N HIS A 291 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 320 through 328 Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing sheet with id= A, first strand: chain 'A' and resid 183 through 187 Processing sheet with id= B, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= C, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= D, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.891A pdb=" N LYS C 104 " --> pdb=" O LEU C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 86 through 91 removed outlier: 6.119A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 6 through 10 Processing sheet with id= G, first strand: chain 'D' and resid 122 through 124 removed outlier: 5.726A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 62 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 5 through 8 Processing sheet with id= I, first strand: chain 'E' and resid 86 through 91 removed outlier: 5.811A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 6 through 10 Processing sheet with id= K, first strand: chain 'F' and resid 124 through 126 removed outlier: 3.795A pdb=" N SER F 36 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 789 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: 4.32 Time building geometry restraints manager: 10.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6480 1.03 - 1.23: 18 1.23 - 1.42: 2983 1.42 - 1.62: 3967 1.62 - 1.81: 51 Bond restraints: 13499 Sorted by residual: bond pdb=" C6 CLR A 608 " pdb=" C7 CLR A 608 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C6 CLR A 607 " pdb=" C7 CLR A 607 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C6 CLR A 605 " pdb=" C7 CLR A 605 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C6 CLR A 604 " pdb=" C7 CLR A 604 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C6 CLR A 606 " pdb=" C7 CLR A 606 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 13494 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.86: 138 104.86 - 112.16: 15036 112.16 - 119.46: 3288 119.46 - 126.76: 5623 126.76 - 134.06: 123 Bond angle restraints: 24208 Sorted by residual: angle pdb=" C22 CLR A 602 " pdb=" C23 CLR A 602 " pdb=" C24 CLR A 602 " ideal model delta sigma weight residual 111.95 103.50 8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" C22 CLR A 605 " pdb=" C23 CLR A 605 " pdb=" C24 CLR A 605 " ideal model delta sigma weight residual 111.95 103.66 8.29 3.00e+00 1.11e-01 7.64e+00 angle pdb=" C22 CLR A 604 " pdb=" C23 CLR A 604 " pdb=" C24 CLR A 604 " ideal model delta sigma weight residual 111.95 103.81 8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" C22 CLR A 603 " pdb=" C23 CLR A 603 " pdb=" C24 CLR A 603 " ideal model delta sigma weight residual 111.95 103.94 8.01 3.00e+00 1.11e-01 7.13e+00 angle pdb=" C22 CLR A 608 " pdb=" C23 CLR A 608 " pdb=" C24 CLR A 608 " ideal model delta sigma weight residual 111.95 104.02 7.93 3.00e+00 1.11e-01 7.00e+00 ... (remaining 24203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6249 17.78 - 35.56: 484 35.56 - 53.34: 112 53.34 - 71.12: 19 71.12 - 88.90: 5 Dihedral angle restraints: 6869 sinusoidal: 3824 harmonic: 3045 Sorted by residual: dihedral pdb=" CA TYR D 55 " pdb=" C TYR D 55 " pdb=" N SER D 56 " pdb=" CA SER D 56 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA HIS A 269 " pdb=" C HIS A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLY C 69 " pdb=" C GLY C 69 " pdb=" N THR C 70 " pdb=" CA THR C 70 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 979 0.080 - 0.161: 86 0.161 - 0.241: 2 0.241 - 0.321: 22 0.321 - 0.402: 8 Chirality restraints: 1097 Sorted by residual: chirality pdb=" C17 CLR A 606 " pdb=" C13 CLR A 606 " pdb=" C16 CLR A 606 " pdb=" C20 CLR A 606 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C17 CLR A 608 " pdb=" C13 CLR A 608 " pdb=" C16 CLR A 608 " pdb=" C20 CLR A 608 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C17 CLR A 604 " pdb=" C13 CLR A 604 " pdb=" C16 CLR A 604 " pdb=" C20 CLR A 604 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1094 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 80 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO E 81 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 12 " -0.111 9.50e-02 1.11e+02 3.70e-02 1.59e+00 pdb=" NE ARG B 12 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 12 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 12 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 12 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B 12 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 12 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 12 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 12 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 41 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.015 5.00e-02 4.00e+02 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2251 2.28 - 2.86: 28817 2.86 - 3.44: 31644 3.44 - 4.02: 45072 4.02 - 4.60: 67774 Nonbonded interactions: 175558 Sorted by model distance: nonbonded pdb=" OE2 GLU F 9 " pdb=" H CYS F 99 " model vdw 1.697 1.850 nonbonded pdb=" HH TYR C 37 " pdb=" OE1 GLN C 90 " model vdw 1.727 1.850 nonbonded pdb=" HE ARG F 41 " pdb=" OE2 GLU F 49 " model vdw 1.762 1.850 nonbonded pdb=" OE1 GLU C 82 " pdb=" H GLU C 82 " model vdw 1.779 1.850 nonbonded pdb="HE22 GLN A 245 " pdb=" O TYR F 104 " model vdw 1.786 1.850 ... (remaining 175553 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 'C' and (resid 3 through 91 or resid 93 through 94 or resid 98 through 10 \ 7)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB \ 3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or \ name HD23)) or resid 56 through 91 or resid 93 through 94 or resid 98 through 1 \ 07)) } ncs_group { reference = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 6 through 31 or resid 33 o \ r resid 35 through 52 or resid 54 or resid 57 through 102 or resid 105 through 1 \ 06 or resid 111 or resid 113 or resid 116 through 127)) selection = (chain 'F' and (resid 5 through 31 or resid 33 or resid 35 through 52 or resid 5 \ 4 or resid 57 through 102 or resid 105 or resid 109 or resid 114 or resid 116 or \ resid 118 through 129)) } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 6.900 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 43.040 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.005 0.049 7008 Z= 0.299 Angle : 0.677 8.449 9592 Z= 0.281 Chirality : 0.067 0.402 1097 Planarity : 0.003 0.049 1131 Dihedral : 13.105 88.900 2881 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.15 (0.31), residues: 819 helix: 1.65 (0.35), residues: 239 sheet: 0.12 (0.38), residues: 216 loop : -0.94 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.004 0.001 HIS A 121 PHE 0.008 0.001 PHE A 53 TYR 0.009 0.001 TYR D 55 ARG 0.005 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8507 (t80) cc_final: 0.8295 (t80) REVERT: A 79 THR cc_start: 0.8984 (p) cc_final: 0.8759 (p) REVERT: C 107 ILE cc_start: 0.7209 (mp) cc_final: 0.6672 (mp) REVERT: F 93 ASP cc_start: 0.8440 (t0) cc_final: 0.8014 (t0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4189 time to fit residues: 77.5952 Evaluate side-chains 117 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7008 Z= 0.170 Angle : 0.472 4.795 9592 Z= 0.251 Chirality : 0.039 0.134 1097 Planarity : 0.003 0.035 1131 Dihedral : 5.494 58.372 1438 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.69 % Allowed : 6.45 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.14 (0.31), residues: 819 helix: 1.65 (0.35), residues: 241 sheet: 0.03 (0.37), residues: 225 loop : -0.93 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 231 TYR 0.009 0.001 TYR D 53 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 93 ASP cc_start: 0.8405 (t0) cc_final: 0.8168 (t0) outliers start: 5 outliers final: 5 residues processed: 127 average time/residue: 0.3903 time to fit residues: 66.8356 Evaluate side-chains 118 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 64 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7008 Z= 0.173 Angle : 0.453 5.891 9592 Z= 0.240 Chirality : 0.039 0.132 1097 Planarity : 0.003 0.034 1131 Dihedral : 5.080 54.733 1438 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.37 % Allowed : 8.09 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.16 (0.31), residues: 819 helix: 1.66 (0.35), residues: 242 sheet: 0.01 (0.36), residues: 226 loop : -0.90 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 107 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 231 TYR 0.009 0.001 TYR D 53 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7073 (tm-30) REVERT: F 93 ASP cc_start: 0.8384 (t0) cc_final: 0.8068 (t0) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.3943 time to fit residues: 62.5604 Evaluate side-chains 116 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 4 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7008 Z= 0.273 Angle : 0.493 5.812 9592 Z= 0.263 Chirality : 0.039 0.134 1097 Planarity : 0.003 0.033 1131 Dihedral : 5.151 50.551 1438 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.06 % Allowed : 9.88 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.02 (0.31), residues: 819 helix: 1.56 (0.34), residues: 242 sheet: -0.11 (0.36), residues: 227 loop : -1.05 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 36 HIS 0.006 0.001 HIS A 121 PHE 0.009 0.001 PHE A 231 TYR 0.013 0.001 TYR D 53 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7237 (tm-30) REVERT: F 93 ASP cc_start: 0.8474 (t0) cc_final: 0.8178 (t0) outliers start: 15 outliers final: 14 residues processed: 121 average time/residue: 0.3875 time to fit residues: 63.2942 Evaluate side-chains 122 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7008 Z= 0.266 Angle : 0.491 6.183 9592 Z= 0.262 Chirality : 0.039 0.135 1097 Planarity : 0.003 0.033 1131 Dihedral : 5.155 45.834 1438 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.78 % Allowed : 10.84 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.03 (0.30), residues: 819 helix: 1.52 (0.34), residues: 242 sheet: -0.11 (0.37), residues: 220 loop : -1.00 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 36 HIS 0.006 0.001 HIS A 121 PHE 0.008 0.001 PHE A 149 TYR 0.013 0.001 TYR D 53 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7216 (tm-30) REVERT: F 93 ASP cc_start: 0.8488 (t0) cc_final: 0.8196 (t0) outliers start: 13 outliers final: 13 residues processed: 119 average time/residue: 0.3817 time to fit residues: 62.3045 Evaluate side-chains 120 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7008 Z= 0.203 Angle : 0.470 6.229 9592 Z= 0.249 Chirality : 0.039 0.132 1097 Planarity : 0.003 0.033 1131 Dihedral : 4.970 41.500 1438 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.19 % Allowed : 11.39 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.10 (0.31), residues: 819 helix: 1.63 (0.35), residues: 240 sheet: -0.03 (0.36), residues: 219 loop : -0.92 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 231 TYR 0.010 0.001 TYR D 53 ARG 0.003 0.000 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7247 (tm-30) REVERT: F 93 ASP cc_start: 0.8527 (t0) cc_final: 0.8195 (t0) outliers start: 16 outliers final: 15 residues processed: 117 average time/residue: 0.3755 time to fit residues: 59.6263 Evaluate side-chains 121 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7008 Z= 0.213 Angle : 0.471 6.338 9592 Z= 0.249 Chirality : 0.039 0.131 1097 Planarity : 0.003 0.033 1131 Dihedral : 4.968 38.669 1438 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.92 % Allowed : 11.93 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.11 (0.31), residues: 819 helix: 1.69 (0.35), residues: 240 sheet: -0.05 (0.36), residues: 219 loop : -0.94 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 231 TYR 0.011 0.001 TYR D 53 ARG 0.003 0.000 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 93 ASP cc_start: 0.8506 (t0) cc_final: 0.8189 (t0) outliers start: 14 outliers final: 14 residues processed: 114 average time/residue: 0.4115 time to fit residues: 64.1956 Evaluate side-chains 119 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.0020 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7008 Z= 0.181 Angle : 0.465 6.333 9592 Z= 0.244 Chirality : 0.039 0.131 1097 Planarity : 0.003 0.033 1131 Dihedral : 4.864 36.709 1438 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.06 % Allowed : 12.48 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.17 (0.31), residues: 819 helix: 1.75 (0.35), residues: 240 sheet: -0.05 (0.36), residues: 219 loop : -0.88 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 231 TYR 0.010 0.001 TYR D 53 ARG 0.002 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7365 (m-80) cc_final: 0.7153 (m-80) REVERT: C 106 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7241 (tm-30) REVERT: F 93 ASP cc_start: 0.8463 (t0) cc_final: 0.8153 (t0) outliers start: 15 outliers final: 13 residues processed: 115 average time/residue: 0.3902 time to fit residues: 60.7024 Evaluate side-chains 119 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7008 Z= 0.189 Angle : 0.468 6.301 9592 Z= 0.246 Chirality : 0.039 0.131 1097 Planarity : 0.003 0.033 1131 Dihedral : 4.864 35.654 1438 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.19 % Allowed : 12.89 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.17 (0.31), residues: 819 helix: 1.78 (0.35), residues: 240 sheet: -0.07 (0.36), residues: 219 loop : -0.90 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 55 TYR 0.011 0.001 TYR D 53 ARG 0.003 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7253 (tm-30) outliers start: 16 outliers final: 15 residues processed: 115 average time/residue: 0.3797 time to fit residues: 59.2997 Evaluate side-chains 119 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7008 Z= 0.149 Angle : 0.455 7.142 9592 Z= 0.238 Chirality : 0.039 0.129 1097 Planarity : 0.003 0.033 1131 Dihedral : 4.696 35.126 1438 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.65 % Allowed : 13.17 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.31), residues: 819 helix: 1.87 (0.35), residues: 240 sheet: 0.02 (0.37), residues: 217 loop : -0.79 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.004 0.001 HIS A 121 PHE 0.008 0.001 PHE A 231 TYR 0.008 0.001 TYR D 53 ARG 0.003 0.000 ARG E 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7232 (tm-30) outliers start: 12 outliers final: 11 residues processed: 113 average time/residue: 0.3916 time to fit residues: 59.8438 Evaluate side-chains 116 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain F residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098567 restraints weight = 28559.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.102753 restraints weight = 15119.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.105434 restraints weight = 9622.440| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7008 Z= 0.186 Angle : 0.465 6.817 9592 Z= 0.244 Chirality : 0.039 0.129 1097 Planarity : 0.003 0.034 1131 Dihedral : 4.741 35.187 1438 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.78 % Allowed : 13.17 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.31), residues: 819 helix: 1.88 (0.35), residues: 240 sheet: 0.08 (0.37), residues: 215 loop : -0.83 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.005 0.001 HIS A 121 PHE 0.008 0.001 PHE A 149 TYR 0.011 0.001 TYR D 53 ARG 0.003 0.000 ARG E 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.47 seconds wall clock time: 61 minutes 24.86 seconds (3684.86 seconds total)