Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 20:44:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/04_2023/7sat_24956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/04_2023/7sat_24956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/04_2023/7sat_24956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/04_2023/7sat_24956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/04_2023/7sat_24956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sat_24956/04_2023/7sat_24956.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1811 atoms to isotropic. 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 41 5.16 5 C 4255 2.51 5 N 1111 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6581 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1704 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "B" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1688 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 3, 'TRANS': 214} Chain: "C" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 612 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "E" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 663 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Time building chain proxies: 3.99, per 1000 atoms: 0.61 Number of scatterers: 6581 At special positions: 0 Unit cell: (86.508, 84.372, 130.296, 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 41 16.00 O 1174 8.00 N 1111 7.00 C 4255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1534 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 Processing helix chain 'A' and resid 31 through 70 removed outlier: 3.610A pdb=" N SER A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 107 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 135 through 148 removed outlier: 4.317A pdb=" N THR A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.665A pdb=" N MET A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.626A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 223 Processing helix chain 'B' and resid 10 through 31 removed outlier: 4.024A pdb=" N MET B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 70 removed outlier: 3.932A pdb=" N LYS B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 98 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.037A pdb=" N GLU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 136 through 154 removed outlier: 4.219A pdb=" N LYS B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 188 through 221 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.577A pdb=" N ALA C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 45 removed outlier: 3.897A pdb=" N LEU C 23 " --> pdb=" O LYS C 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 67 removed outlier: 3.659A pdb=" N MET C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 19 through 43 removed outlier: 3.903A pdb=" N LEU D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 68 removed outlier: 3.964A pdb=" N MET D 52 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE D 54 " --> pdb=" O ASN D 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 17 removed outlier: 3.735A pdb=" N MET E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 44 Processing helix chain 'E' and resid 49 through 67 removed outlier: 3.951A pdb=" N VAL E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.669A pdb=" N TYR F 7 " --> pdb=" O HIS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 44 removed outlier: 3.998A pdb=" N ALA F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 67 removed outlier: 3.594A pdb=" N PHE F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 16 removed outlier: 3.562A pdb=" N ALA G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 45 removed outlier: 3.526A pdb=" N LEU G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 67 441 hydrogen bonds defined for protein. 1314 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: 1.72 Time building geometry restraints manager: 2.74 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: 2077 1.34 - 1.46: 1008 1.46 - 1.57: 3545 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 6710 Sorted by residual: bond pdb=" CG GLU B 209 " pdb=" CD GLU B 209 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CG1 ILE B 15 " pdb=" CD1 ILE B 15 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CA VAL B 151 " pdb=" C VAL B 151 " ideal model delta sigma weight residual 1.518 1.530 -0.012 1.13e-02 7.83e+03 1.10e+00 bond pdb=" CB VAL D 63 " pdb=" CG1 VAL D 63 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB VAL C 35 " pdb=" CG1 VAL C 35 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.97e-01 ... (remaining 6705 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.76: 83 104.76 - 112.08: 3301 112.08 - 119.40: 2228 119.40 - 126.73: 3335 126.73 - 134.05: 87 Bond angle restraints: 9034 Sorted by residual: angle pdb=" N TRP G 30 " pdb=" CA TRP G 30 " pdb=" CB TRP G 30 " ideal model delta sigma weight residual 110.39 116.53 -6.14 1.66e+00 3.63e-01 1.37e+01 angle pdb=" C ARG A 148 " pdb=" N GLU A 149 " pdb=" CA GLU A 149 " ideal model delta sigma weight residual 121.54 128.46 -6.92 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C SER G 29 " pdb=" N TRP G 30 " pdb=" CA TRP G 30 " ideal model delta sigma weight residual 120.72 114.85 5.87 1.67e+00 3.59e-01 1.24e+01 angle pdb=" N ARG B 117 " pdb=" CA ARG B 117 " pdb=" C ARG B 117 " ideal model delta sigma weight residual 113.43 109.25 4.18 1.26e+00 6.30e-01 1.10e+01 angle pdb=" N ASP A 115 " pdb=" CA ASP A 115 " pdb=" C ASP A 115 " ideal model delta sigma weight residual 114.64 109.78 4.86 1.52e+00 4.33e-01 1.02e+01 ... (remaining 9029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 3380 14.04 - 28.08: 450 28.08 - 42.12: 151 42.12 - 56.16: 23 56.16 - 70.20: 10 Dihedral angle restraints: 4014 sinusoidal: 1632 harmonic: 2382 Sorted by residual: dihedral pdb=" CA LYS B 99 " pdb=" C LYS B 99 " pdb=" N LEU B 100 " pdb=" CA LEU B 100 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA TRP A 179 " pdb=" C TRP A 179 " pdb=" N GLU A 180 " pdb=" CA GLU A 180 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU B 161 " pdb=" C LEU B 161 " pdb=" N LYS B 162 " pdb=" CA LYS B 162 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 818 0.048 - 0.097: 169 0.097 - 0.145: 21 0.145 - 0.194: 3 0.194 - 0.242: 1 Chirality restraints: 1012 Sorted by residual: chirality pdb=" CA TRP G 30 " pdb=" N TRP G 30 " pdb=" C TRP G 30 " pdb=" CB TRP G 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU A 87 " pdb=" N GLU A 87 " pdb=" C GLU A 87 " pdb=" CB GLU A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CB ILE A 15 " pdb=" CA ILE A 15 " pdb=" CG1 ILE A 15 " pdb=" CG2 ILE A 15 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 1009 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 30 " 0.039 2.00e-02 2.50e+03 3.50e-02 3.07e+01 pdb=" CG TRP G 30 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 TRP G 30 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP G 30 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 30 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 30 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 30 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 30 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 30 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP G 30 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 46 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO E 47 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO E 47 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 47 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 83 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C VAL A 83 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL A 83 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 84 " -0.014 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 111 2.64 - 3.21: 6605 3.21 - 3.77: 10371 3.77 - 4.34: 13204 4.34 - 4.90: 21473 Nonbonded interactions: 51764 Sorted by model distance: nonbonded pdb=" OG SER A 181 " pdb=" OE1 GLU A 185 " model vdw 2.080 2.440 nonbonded pdb=" OD1 ASN A 64 " pdb=" OH TYR A 78 " model vdw 2.151 2.440 nonbonded pdb=" O VAL F 63 " pdb=" OG SER F 67 " model vdw 2.208 2.440 nonbonded pdb=" NZ LYS A 99 " pdb=" OE1 GLN A 200 " model vdw 2.250 2.520 nonbonded pdb=" O ASP B 89 " pdb=" OG1 THR B 93 " model vdw 2.264 2.440 ... (remaining 51759 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' and resid 5 through 221) selection = (chain 'B' and resid 5 through 221) } ncs_group { reference = (chain 'C' and resid 5 through 78) selection = chain 'D' selection = (chain 'E' and resid 5 through 78) selection = (chain 'F' and resid 5 through 78) selection = (chain 'G' and resid 5 through 78) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.250 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 6710 Z= 0.254 Angle : 0.755 10.464 9034 Z= 0.409 Chirality : 0.040 0.242 1012 Planarity : 0.004 0.081 1122 Dihedral : 14.441 70.198 2480 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 808 helix: 1.09 (0.22), residues: 573 sheet: None (None), residues: 0 loop : -2.67 (0.39), residues: 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 281 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 281 average time/residue: 0.1992 time to fit residues: 72.0667 Evaluate side-chains 235 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6710 Z= 0.208 Angle : 0.689 11.681 9034 Z= 0.349 Chirality : 0.038 0.157 1012 Planarity : 0.004 0.056 1122 Dihedral : 4.596 19.803 888 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.30), residues: 808 helix: 1.30 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.99 (0.41), residues: 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 261 time to evaluate : 0.817 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 272 average time/residue: 0.1961 time to fit residues: 68.8915 Evaluate side-chains 253 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 234 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0618 time to fit residues: 3.0971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6710 Z= 0.203 Angle : 0.683 11.511 9034 Z= 0.341 Chirality : 0.038 0.148 1012 Planarity : 0.004 0.049 1122 Dihedral : 4.460 19.740 888 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 808 helix: 1.43 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.98 (0.40), residues: 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 267 average time/residue: 0.1981 time to fit residues: 68.3331 Evaluate side-chains 234 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 230 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0636 time to fit residues: 1.5763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0000 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6710 Z= 0.187 Angle : 0.723 14.653 9034 Z= 0.350 Chirality : 0.038 0.179 1012 Planarity : 0.003 0.047 1122 Dihedral : 4.345 18.770 888 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 808 helix: 1.42 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -2.94 (0.40), residues: 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 262 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 267 average time/residue: 0.1954 time to fit residues: 67.9117 Evaluate side-chains 249 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 238 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0977 time to fit residues: 2.7675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.0050 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN B 29 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6710 Z= 0.188 Angle : 0.726 11.888 9034 Z= 0.356 Chirality : 0.039 0.196 1012 Planarity : 0.004 0.046 1122 Dihedral : 4.318 18.419 888 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 808 helix: 1.42 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.90 (0.39), residues: 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 269 average time/residue: 0.1998 time to fit residues: 68.9958 Evaluate side-chains 243 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0659 time to fit residues: 1.2221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6710 Z= 0.193 Angle : 0.732 12.292 9034 Z= 0.358 Chirality : 0.039 0.203 1012 Planarity : 0.003 0.044 1122 Dihedral : 4.301 17.944 888 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 808 helix: 1.48 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.82 (0.39), residues: 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 264 time to evaluate : 0.858 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 266 average time/residue: 0.1959 time to fit residues: 67.3747 Evaluate side-chains 252 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0694 time to fit residues: 1.6021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 0.0030 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6710 Z= 0.197 Angle : 0.755 12.871 9034 Z= 0.369 Chirality : 0.041 0.235 1012 Planarity : 0.003 0.044 1122 Dihedral : 4.333 18.218 888 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 808 helix: 1.57 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -2.81 (0.39), residues: 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 269 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 272 average time/residue: 0.2053 time to fit residues: 74.0699 Evaluate side-chains 252 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 249 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0656 time to fit residues: 1.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 37 optimal weight: 0.0040 chunk 7 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.0770 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6710 Z= 0.190 Angle : 0.777 12.447 9034 Z= 0.382 Chirality : 0.041 0.238 1012 Planarity : 0.004 0.041 1122 Dihedral : 4.384 17.604 888 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.56 % 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: 0.66 (0.30), residues: 808 helix: 1.47 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -2.76 (0.40), residues: 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 264 average time/residue: 0.1835 time to fit residues: 63.3910 Evaluate side-chains 250 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0768 time to fit residues: 1.4342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 6710 Z= 0.214 Angle : 0.815 13.219 9034 Z= 0.395 Chirality : 0.042 0.230 1012 Planarity : 0.004 0.045 1122 Dihedral : 4.379 17.273 888 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.56 % 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: 0.59 (0.30), residues: 808 helix: 1.51 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.91 (0.38), residues: 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 253 average time/residue: 0.1886 time to fit residues: 61.9787 Evaluate side-chains 246 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 243 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0883 time to fit residues: 1.5057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 6710 Z= 0.221 Angle : 0.844 13.723 9034 Z= 0.407 Chirality : 0.043 0.250 1012 Planarity : 0.004 0.046 1122 Dihedral : 4.438 17.560 888 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.29), residues: 808 helix: 1.37 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -2.97 (0.37), residues: 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 247 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 249 average time/residue: 0.1946 time to fit residues: 63.5180 Evaluate side-chains 245 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0791 time to fit residues: 1.8274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.125926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100084 restraints weight = 13330.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102681 restraints weight = 8294.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104464 restraints weight = 6026.193| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 6710 Z= 0.234 Angle : 0.844 13.771 9034 Z= 0.408 Chirality : 0.043 0.259 1012 Planarity : 0.004 0.045 1122 Dihedral : 4.478 17.562 888 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 808 helix: 1.32 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -2.96 (0.37), residues: 217 =============================================================================== Job complete usr+sys time: 1775.44 seconds wall clock time: 32 minutes 45.39 seconds (1965.39 seconds total)