Starting phenix.real_space_refine on Mon May 6 21:19:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/05_2024/7cxr_30495.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/05_2024/7cxr_30495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/05_2024/7cxr_30495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/05_2024/7cxr_30495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/05_2024/7cxr_30495.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/05_2024/7cxr_30495.pdb" } resolution = 3.4 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= 0.003 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3406 2.51 5 N 858 2.21 5 O 876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 5168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2584 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 7, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2584 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 7, 'TRANS': 299} Chain breaks: 1 Time building chain proxies: 3.19, per 1000 atoms: 0.62 Number of scatterers: 5168 At special positions: 0 Unit cell: (90.221, 114.135, 93.482, 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 28 16.00 O 876 8.00 N 858 7.00 C 3406 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: 1.96 Conformation dependent library (CDL) restraints added in 798.0 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 9 through 69 removed outlier: 3.811A pdb=" N GLN A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 99 removed outlier: 3.594A pdb=" N LYS A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 157 through 186 Processing helix chain 'A' and resid 191 through 208 removed outlier: 4.360A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 236 removed outlier: 5.740A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 4.386A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 removed outlier: 4.138A pdb=" N THR A 273 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 305 through 338 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 69 removed outlier: 3.811A pdb=" N GLN B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 58 " --> pdb=" O GLN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 99 removed outlier: 3.594A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 157 through 186 Processing helix chain 'B' and resid 191 through 208 removed outlier: 4.360A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 202 " --> pdb=" O TYR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 236 removed outlier: 5.740A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 4.386A pdb=" N TYR B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 297 removed outlier: 4.137A pdb=" N THR B 273 " --> pdb=" O TRP B 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 305 through 338 Proline residue: B 313 - end of helix 422 hydrogen bonds defined for protein. 1266 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: 1.50 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 788 1.32 - 1.44: 1614 1.44 - 1.57: 2870 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5314 Sorted by residual: bond pdb=" C ILE A 181 " pdb=" O ILE A 181 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" C ILE B 181 " pdb=" O ILE B 181 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N ILE A 181 " pdb=" CA ILE A 181 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N ILE B 181 " pdb=" CA ILE B 181 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" C PRO B 313 " pdb=" O PRO B 313 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.30e-02 5.92e+03 9.36e+00 ... (remaining 5309 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.04: 74 106.04 - 113.10: 2752 113.10 - 120.16: 2219 120.16 - 127.22: 2071 127.22 - 134.29: 60 Bond angle restraints: 7176 Sorted by residual: angle pdb=" N ILE B 181 " pdb=" CA ILE B 181 " pdb=" C ILE B 181 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.93e+01 angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 110.62 104.93 5.69 1.02e+00 9.61e-01 3.12e+01 angle pdb=" CA LEU B 121 " pdb=" C LEU B 121 " pdb=" O LEU B 121 " ideal model delta sigma weight residual 122.03 115.76 6.27 1.17e+00 7.31e-01 2.87e+01 angle pdb=" CA LEU A 121 " pdb=" C LEU A 121 " pdb=" O LEU A 121 " ideal model delta sigma weight residual 122.03 115.97 6.06 1.17e+00 7.31e-01 2.68e+01 angle pdb=" C THR B 48 " pdb=" CA THR B 48 " pdb=" CB THR B 48 " ideal model delta sigma weight residual 110.68 117.80 -7.12 1.70e+00 3.46e-01 1.76e+01 ... (remaining 7171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 2617 16.42 - 32.84: 368 32.84 - 49.26: 72 49.26 - 65.68: 25 65.68 - 82.10: 10 Dihedral angle restraints: 3092 sinusoidal: 1282 harmonic: 1810 Sorted by residual: dihedral pdb=" C LEU A 58 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " pdb=" CB LEU A 58 " ideal model delta harmonic sigma weight residual -122.60 -112.58 -10.02 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" C LEU B 58 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " pdb=" CB LEU B 58 " ideal model delta harmonic sigma weight residual -122.60 -112.87 -9.73 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CA LEU A 58 " pdb=" CB LEU A 58 " ideal model delta harmonic sigma weight residual 122.80 113.45 9.35 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 3089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 668 0.070 - 0.139: 77 0.139 - 0.209: 10 0.209 - 0.279: 7 0.279 - 0.349: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA LEU B 58 " pdb=" N LEU B 58 " pdb=" C LEU B 58 " pdb=" CB LEU B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA GLN A 44 " pdb=" N GLN A 44 " pdb=" C GLN A 44 " pdb=" CB GLN A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 761 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 46 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ASN A 46 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN A 46 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS A 47 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 120 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C LEU B 120 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU B 120 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 121 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 120 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C LEU A 120 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 120 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 121 " -0.012 2.00e-02 2.50e+03 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 582 2.74 - 3.28: 5643 3.28 - 3.82: 8714 3.82 - 4.36: 9209 4.36 - 4.90: 15363 Nonbonded interactions: 39511 Sorted by model distance: nonbonded pdb=" NE2 GLN A 222 " pdb=" OD1 ASN A 289 " model vdw 2.199 2.520 nonbonded pdb=" NE2 GLN B 222 " pdb=" OD1 ASN B 289 " model vdw 2.200 2.520 nonbonded pdb=" ND2 ASN A 105 " pdb=" O VAL A 116 " model vdw 2.208 2.520 nonbonded pdb=" ND2 ASN B 105 " pdb=" O VAL B 116 " model vdw 2.209 2.520 nonbonded pdb=" O ILE A 183 " pdb=" NH1 ARG A 188 " model vdw 2.257 2.520 ... (remaining 39506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.390 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.940 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 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 : 0.007 0.043 5314 Z= 0.443 Angle : 0.874 7.125 7176 Z= 0.568 Chirality : 0.057 0.349 764 Planarity : 0.005 0.037 892 Dihedral : 16.560 82.104 1920 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.60 % Favored : 93.07 % Rotamer: Outliers : 3.39 % Allowed : 11.96 % Favored : 84.64 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.30), residues: 606 helix: -1.00 (0.20), residues: 502 sheet: None (None), residues: 0 loop : -3.24 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 285 HIS 0.003 0.001 HIS A 30 PHE 0.016 0.002 PHE A 23 TYR 0.019 0.002 TYR A 171 ARG 0.002 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: -0.0530 (OUTLIER) cc_final: -0.1005 (tp) REVERT: A 98 GLU cc_start: 0.8125 (tt0) cc_final: 0.7550 (tp30) REVERT: A 137 LYS cc_start: 0.7918 (tttt) cc_final: 0.7714 (ttpp) REVERT: A 232 PHE cc_start: 0.7338 (t80) cc_final: 0.6904 (t80) REVERT: B 9 LEU cc_start: -0.1407 (OUTLIER) cc_final: -0.1685 (tp) REVERT: B 104 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8139 (tptp) REVERT: B 204 SER cc_start: 0.8748 (t) cc_final: 0.8494 (t) REVERT: B 232 PHE cc_start: 0.7580 (t80) cc_final: 0.7107 (t80) REVERT: B 236 LEU cc_start: 0.8187 (mt) cc_final: 0.7612 (tt) outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 0.2272 time to fit residues: 40.2299 Evaluate side-chains 105 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 242 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 44 GLN A 165 ASN A 230 GLN A 334 HIS B 44 GLN B 165 ASN B 185 ASN B 241 GLN B 334 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5314 Z= 0.218 Angle : 0.653 6.293 7176 Z= 0.337 Chirality : 0.040 0.158 764 Planarity : 0.004 0.037 892 Dihedral : 5.140 51.187 676 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.86 % Allowed : 20.18 % Favored : 76.96 % 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: 0.80 (0.34), residues: 606 helix: 1.16 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.86 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 285 HIS 0.002 0.001 HIS B 283 PHE 0.014 0.001 PHE B 23 TYR 0.021 0.002 TYR A 239 ARG 0.003 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8240 (tt0) cc_final: 0.7692 (tp30) REVERT: A 182 LEU cc_start: 0.8453 (tp) cc_final: 0.8177 (mt) REVERT: A 232 PHE cc_start: 0.7265 (t80) cc_final: 0.6891 (t80) REVERT: A 241 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6509 (mp10) REVERT: B 9 LEU cc_start: -0.1453 (OUTLIER) cc_final: -0.1863 (tp) REVERT: B 98 GLU cc_start: 0.8441 (tt0) cc_final: 0.8075 (tp30) REVERT: B 104 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8144 (tptp) REVERT: B 127 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7556 (t80) REVERT: B 232 PHE cc_start: 0.7422 (t80) cc_final: 0.7210 (t80) REVERT: B 236 LEU cc_start: 0.7971 (mt) cc_final: 0.7495 (tt) outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 0.2051 time to fit residues: 28.5745 Evaluate side-chains 100 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 294 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.0000 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 197 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS B 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5314 Z= 0.195 Angle : 0.608 8.077 7176 Z= 0.309 Chirality : 0.037 0.140 764 Planarity : 0.004 0.040 892 Dihedral : 4.446 21.733 672 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.14 % Allowed : 22.68 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.35), residues: 606 helix: 1.87 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.96 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 210 HIS 0.002 0.001 HIS A 283 PHE 0.016 0.001 PHE B 23 TYR 0.015 0.001 TYR B 239 ARG 0.005 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8367 (tt0) cc_final: 0.8045 (tp30) REVERT: A 210 TRP cc_start: 0.7148 (t-100) cc_final: 0.6169 (m-90) REVERT: A 232 PHE cc_start: 0.7325 (t80) cc_final: 0.6948 (t80) REVERT: A 312 PHE cc_start: 0.7782 (m-10) cc_final: 0.7475 (m-10) REVERT: B 36 LYS cc_start: 0.6731 (mttm) cc_final: 0.6351 (mttm) REVERT: B 104 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8014 (tptp) REVERT: B 127 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 236 LEU cc_start: 0.7874 (mt) cc_final: 0.7513 (tt) outliers start: 12 outliers final: 5 residues processed: 117 average time/residue: 0.2399 time to fit residues: 35.0314 Evaluate side-chains 100 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5314 Z= 0.164 Angle : 0.569 6.960 7176 Z= 0.292 Chirality : 0.037 0.147 764 Planarity : 0.004 0.038 892 Dihedral : 4.110 21.663 668 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.39 % Allowed : 23.39 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.35), residues: 606 helix: 2.26 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.76 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 285 HIS 0.002 0.000 HIS A 283 PHE 0.013 0.001 PHE B 312 TYR 0.011 0.001 TYR A 239 ARG 0.003 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7363 (mtp85) REVERT: A 98 GLU cc_start: 0.8299 (tt0) cc_final: 0.8034 (tp30) REVERT: A 210 TRP cc_start: 0.7138 (t-100) cc_final: 0.6186 (m-90) REVERT: A 268 MET cc_start: 0.5118 (tpt) cc_final: 0.4705 (mpp) REVERT: A 312 PHE cc_start: 0.7819 (m-10) cc_final: 0.7468 (m-10) REVERT: B 127 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7570 (t80) REVERT: B 207 MET cc_start: 0.7008 (tpp) cc_final: 0.6644 (tmm) REVERT: B 316 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7223 (mp) outliers start: 19 outliers final: 9 residues processed: 109 average time/residue: 0.2195 time to fit residues: 29.6717 Evaluate side-chains 103 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS B 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5314 Z= 0.239 Angle : 0.664 7.247 7176 Z= 0.344 Chirality : 0.040 0.177 764 Planarity : 0.004 0.040 892 Dihedral : 4.365 21.274 668 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.21 % Allowed : 26.25 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.35), residues: 606 helix: 1.96 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.66 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 285 HIS 0.003 0.001 HIS A 283 PHE 0.011 0.001 PHE B 94 TYR 0.012 0.001 TYR B 171 ARG 0.006 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8486 (tt0) cc_final: 0.8228 (tp30) REVERT: A 210 TRP cc_start: 0.7296 (t-100) cc_final: 0.6274 (m-90) REVERT: A 268 MET cc_start: 0.4524 (tpt) cc_final: 0.4305 (mpp) REVERT: A 312 PHE cc_start: 0.8140 (m-10) cc_final: 0.7726 (m-10) REVERT: B 127 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7553 (t80) REVERT: B 160 THR cc_start: 0.8769 (m) cc_final: 0.8520 (p) REVERT: B 215 MET cc_start: 0.6219 (mmm) cc_final: 0.5917 (mmp) REVERT: B 316 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7411 (mp) outliers start: 18 outliers final: 10 residues processed: 117 average time/residue: 0.2105 time to fit residues: 30.3314 Evaluate side-chains 102 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5314 Z= 0.199 Angle : 0.616 6.839 7176 Z= 0.317 Chirality : 0.039 0.145 764 Planarity : 0.004 0.040 892 Dihedral : 4.127 18.025 666 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.46 % Allowed : 26.25 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.35), residues: 606 helix: 2.09 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.56 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 16 HIS 0.002 0.000 HIS A 196 PHE 0.020 0.001 PHE B 23 TYR 0.010 0.001 TYR A 239 ARG 0.004 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7396 (mtp85) REVERT: A 98 GLU cc_start: 0.8515 (tt0) cc_final: 0.8270 (tp30) REVERT: A 210 TRP cc_start: 0.7334 (t-100) cc_final: 0.6377 (m-90) REVERT: A 268 MET cc_start: 0.5183 (tpt) cc_final: 0.4617 (mpp) REVERT: A 298 GLN cc_start: 0.6220 (OUTLIER) cc_final: 0.5786 (tp40) REVERT: A 312 PHE cc_start: 0.8099 (m-10) cc_final: 0.7616 (m-10) REVERT: B 98 GLU cc_start: 0.8781 (tp30) cc_final: 0.8482 (tp30) REVERT: B 127 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7476 (t80) REVERT: B 210 TRP cc_start: 0.7558 (t-100) cc_final: 0.6618 (m-90) REVERT: B 215 MET cc_start: 0.5872 (mmm) cc_final: 0.5512 (mmp) outliers start: 25 outliers final: 7 residues processed: 115 average time/residue: 0.1891 time to fit residues: 27.3693 Evaluate side-chains 99 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5314 Z= 0.254 Angle : 0.686 9.905 7176 Z= 0.355 Chirality : 0.041 0.167 764 Planarity : 0.004 0.041 892 Dihedral : 4.347 19.076 666 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.18 % Allowed : 25.71 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.34), residues: 606 helix: 1.81 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.64 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 16 HIS 0.003 0.001 HIS B 283 PHE 0.023 0.002 PHE B 23 TYR 0.011 0.001 TYR A 239 ARG 0.009 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8584 (tt0) cc_final: 0.8338 (tp30) REVERT: A 210 TRP cc_start: 0.7402 (t-100) cc_final: 0.6335 (m-90) REVERT: A 268 MET cc_start: 0.4634 (tpt) cc_final: 0.4366 (mpp) REVERT: A 298 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5770 (tp40) REVERT: A 312 PHE cc_start: 0.8030 (m-10) cc_final: 0.7545 (m-10) REVERT: B 98 GLU cc_start: 0.8817 (tp30) cc_final: 0.8563 (tp30) REVERT: B 127 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 203 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7844 (tp) REVERT: B 210 TRP cc_start: 0.7643 (t-100) cc_final: 0.6731 (m-90) outliers start: 29 outliers final: 16 residues processed: 113 average time/residue: 0.1781 time to fit residues: 25.8069 Evaluate side-chains 100 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5314 Z= 0.184 Angle : 0.650 11.338 7176 Z= 0.326 Chirality : 0.039 0.154 764 Planarity : 0.004 0.047 892 Dihedral : 4.190 18.521 666 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.50 % Allowed : 28.57 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.35), residues: 606 helix: 2.03 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.52 (0.63), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 16 HIS 0.002 0.000 HIS B 30 PHE 0.021 0.001 PHE B 23 TYR 0.024 0.001 TYR A 100 ARG 0.006 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8610 (tt0) cc_final: 0.8408 (mm-30) REVERT: A 268 MET cc_start: 0.5146 (tpt) cc_final: 0.4603 (mpp) REVERT: A 312 PHE cc_start: 0.8043 (m-10) cc_final: 0.7775 (m-10) REVERT: B 98 GLU cc_start: 0.8877 (tp30) cc_final: 0.8604 (tp30) REVERT: B 127 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7445 (t80) REVERT: B 203 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7704 (tp) REVERT: B 210 TRP cc_start: 0.7526 (t-100) cc_final: 0.6627 (m-90) REVERT: B 298 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5371 (tp40) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.1914 time to fit residues: 23.6552 Evaluate side-chains 92 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5314 Z= 0.214 Angle : 0.669 8.877 7176 Z= 0.339 Chirality : 0.040 0.168 764 Planarity : 0.004 0.056 892 Dihedral : 4.248 19.030 666 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.93 % Allowed : 27.68 % Favored : 68.39 % 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: 1.97 (0.34), residues: 606 helix: 1.93 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.51 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 16 HIS 0.003 0.001 HIS A 283 PHE 0.022 0.001 PHE B 23 TYR 0.013 0.001 TYR A 100 ARG 0.004 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.4668 (tpt) cc_final: 0.4458 (mpp) REVERT: A 291 LEU cc_start: 0.7396 (tp) cc_final: 0.6716 (mp) REVERT: A 298 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.5792 (tp40) REVERT: B 98 GLU cc_start: 0.8879 (tp30) cc_final: 0.8643 (tp30) REVERT: B 127 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7555 (t80) REVERT: B 203 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7714 (tp) REVERT: B 210 TRP cc_start: 0.7584 (t-100) cc_final: 0.6856 (m-90) REVERT: B 298 GLN cc_start: 0.5788 (OUTLIER) cc_final: 0.5335 (tp40) outliers start: 22 outliers final: 15 residues processed: 104 average time/residue: 0.1850 time to fit residues: 25.2661 Evaluate side-chains 107 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5314 Z= 0.206 Angle : 0.671 10.226 7176 Z= 0.338 Chirality : 0.040 0.175 764 Planarity : 0.004 0.056 892 Dihedral : 4.242 19.243 666 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.57 % Allowed : 28.21 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.35), residues: 606 helix: 1.96 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.45 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 16 HIS 0.002 0.000 HIS B 283 PHE 0.022 0.001 PHE B 23 TYR 0.010 0.001 TYR A 100 ARG 0.004 0.001 ARG B 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7539 (mtp85) REVERT: A 268 MET cc_start: 0.5212 (tpt) cc_final: 0.4572 (mpp) REVERT: A 291 LEU cc_start: 0.7381 (tp) cc_final: 0.6722 (mp) REVERT: A 298 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5766 (tp40) REVERT: B 98 GLU cc_start: 0.8871 (tp30) cc_final: 0.8390 (tp30) REVERT: B 127 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7545 (t80) REVERT: B 203 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7752 (tp) REVERT: B 210 TRP cc_start: 0.7643 (t-100) cc_final: 0.6917 (m-90) REVERT: B 298 GLN cc_start: 0.5768 (OUTLIER) cc_final: 0.5332 (tp40) outliers start: 20 outliers final: 14 residues processed: 100 average time/residue: 0.1508 time to fit residues: 19.9342 Evaluate side-chains 105 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.260698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.240576 restraints weight = 7769.943| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 1.85 r_work: 0.4540 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5314 Z= 0.187 Angle : 0.647 9.581 7176 Z= 0.324 Chirality : 0.039 0.192 764 Planarity : 0.004 0.058 892 Dihedral : 4.091 19.141 666 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.04 % Allowed : 28.39 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.35), residues: 606 helix: 2.13 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.43 (0.63), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 16 HIS 0.002 0.000 HIS A 283 PHE 0.022 0.001 PHE B 23 TYR 0.010 0.001 TYR B 33 ARG 0.002 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.86 seconds wall clock time: 28 minutes 40.13 seconds (1720.13 seconds total)