Starting phenix.real_space_refine on Thu Mar 6 06:08:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cxr_30495/03_2025/7cxr_30495.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cxr_30495/03_2025/7cxr_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/cci-nas-00/data/ceres_data/7cxr_30495/03_2025/7cxr_30495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cxr_30495/03_2025/7cxr_30495.map" model { file = "/net/cci-nas-00/data/ceres_data/7cxr_30495/03_2025/7cxr_30495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cxr_30495/03_2025/7cxr_30495.cif" } 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. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.71, per 1000 atoms: 0.72 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 - 3.00 Amino acid : True - 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: 1.49 Conformation dependent library (CDL) restraints added in 985.1 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: 0.43 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: 1.88 Time building geometry restraints manager: 1.76 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: 0.00 - 1.43: 6582 1.43 - 2.85: 448 2.85 - 4.27: 115 4.27 - 5.70: 27 5.70 - 7.12: 4 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 3.120 nonbonded pdb=" NE2 GLN B 222 " pdb=" OD1 ASN B 289 " model vdw 2.200 3.120 nonbonded pdb=" ND2 ASN A 105 " pdb=" O VAL A 116 " model vdw 2.208 3.120 nonbonded pdb=" ND2 ASN B 105 " pdb=" O VAL B 116 " model vdw 2.209 3.120 nonbonded pdb=" O ILE A 183 " pdb=" NH1 ARG A 188 " model vdw 2.257 3.120 ... (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 Time spend for trying shortcut: 0.03 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: 26.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:3.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.320 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.517 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: 0.2609 time to fit residues: 46.3668 Evaluate side-chains 105 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 0.0970 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 230 GLN A 334 HIS B 44 GLN B 185 ASN B 222 GLN B 241 GLN B 334 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.272311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.250433 restraints weight = 7789.601| |-----------------------------------------------------------------------------| r_work (start): 0.4720 rms_B_bonded: 1.78 r_work: 0.4642 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5314 Z= 0.239 Angle : 0.687 6.352 7176 Z= 0.355 Chirality : 0.041 0.168 764 Planarity : 0.005 0.036 892 Dihedral : 5.142 44.976 676 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.68 % Allowed : 20.36 % 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: 0.79 (0.34), residues: 606 helix: 1.15 (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 0.018 0.002 TRP A 285 HIS 0.003 0.001 HIS B 283 PHE 0.016 0.001 PHE B 312 TYR 0.021 0.002 TYR A 239 ARG 0.005 0.001 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 111 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8255 (tt0) cc_final: 0.7849 (tp30) REVERT: A 182 LEU cc_start: 0.8488 (tp) cc_final: 0.8246 (mt) REVERT: A 232 PHE cc_start: 0.7459 (t80) cc_final: 0.7094 (t80) REVERT: A 241 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6457 (mp10) REVERT: A 312 PHE cc_start: 0.7937 (m-10) cc_final: 0.7685 (m-10) REVERT: B 9 LEU cc_start: -0.0953 (OUTLIER) cc_final: -0.1543 (tp) REVERT: B 127 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7521 (t80) REVERT: B 236 LEU cc_start: 0.7808 (mt) cc_final: 0.7599 (tt) outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 0.2699 time to fit residues: 36.9389 Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 294 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 222 GLN B 196 HIS B 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.267974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.246240 restraints weight = 7698.831| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 1.83 r_work: 0.4574 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5314 Z= 0.254 Angle : 0.668 6.978 7176 Z= 0.344 Chirality : 0.040 0.145 764 Planarity : 0.004 0.041 892 Dihedral : 4.612 20.979 672 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.04 % Allowed : 22.86 % Favored : 74.11 % 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: 1.44 (0.35), residues: 606 helix: 1.63 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.98 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 210 HIS 0.003 0.001 HIS A 283 PHE 0.019 0.001 PHE B 23 TYR 0.013 0.001 TYR A 133 ARG 0.003 0.001 ARG B 31 *********************** 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 119 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7183 (t-100) cc_final: 0.6412 (m-90) REVERT: B 39 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: B 75 GLU cc_start: -0.0601 (OUTLIER) cc_final: -0.1080 (pt0) REVERT: B 127 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 215 MET cc_start: 0.5788 (mmm) cc_final: 0.5581 (mmp) REVERT: B 316 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7677 (mp) outliers start: 17 outliers final: 7 residues processed: 114 average time/residue: 0.2095 time to fit residues: 31.5517 Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 75 GLU 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 316 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.269583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.247801 restraints weight = 7730.461| |-----------------------------------------------------------------------------| r_work (start): 0.4666 rms_B_bonded: 2.01 r_work: 0.4581 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5314 Z= 0.197 Angle : 0.616 7.157 7176 Z= 0.316 Chirality : 0.038 0.142 764 Planarity : 0.004 0.040 892 Dihedral : 4.144 17.645 666 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.68 % Allowed : 24.29 % Favored : 73.04 % 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: 1.95 (0.35), residues: 606 helix: 1.93 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.52 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.020 0.001 PHE A 232 TYR 0.012 0.001 TYR B 33 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 115 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7399 (t-100) cc_final: 0.6638 (m-90) REVERT: A 312 PHE cc_start: 0.8117 (m-10) cc_final: 0.7759 (m-10) REVERT: B 75 GLU cc_start: 0.0123 (OUTLIER) cc_final: -0.0347 (pt0) REVERT: B 127 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7542 (t80) outliers start: 15 outliers final: 8 residues processed: 108 average time/residue: 0.2166 time to fit residues: 29.2396 Evaluate side-chains 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 228 MET Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 75 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.0070 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.266645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.245094 restraints weight = 7852.301| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 1.85 r_work: 0.4599 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.5653 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= 0.193 Angle : 0.611 7.080 7176 Z= 0.313 Chirality : 0.038 0.145 764 Planarity : 0.004 0.041 892 Dihedral : 4.098 17.653 666 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.93 % Allowed : 24.64 % Favored : 71.43 % 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: 514 sheet: None (None), residues: 0 loop : -2.41 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.015 0.001 PHE A 232 TYR 0.009 0.001 TYR A 239 ARG 0.004 0.000 ARG A 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 119 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7335 (t-100) cc_final: 0.6685 (m-90) REVERT: A 312 PHE cc_start: 0.8247 (m-10) cc_final: 0.7920 (m-10) REVERT: B 75 GLU cc_start: -0.0271 (OUTLIER) cc_final: -0.0651 (pt0) REVERT: B 127 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7439 (t80) REVERT: B 210 TRP cc_start: 0.7629 (t-100) cc_final: 0.6951 (m-90) outliers start: 22 outliers final: 11 residues processed: 109 average time/residue: 0.2549 time to fit residues: 34.4864 Evaluate side-chains 102 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 75 GLU 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 294 PHE Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 44 GLN B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.263708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.242800 restraints weight = 7759.379| |-----------------------------------------------------------------------------| r_work (start): 0.4654 rms_B_bonded: 1.86 r_work: 0.4575 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.6105 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= 0.220 Angle : 0.656 6.800 7176 Z= 0.332 Chirality : 0.039 0.162 764 Planarity : 0.004 0.041 892 Dihedral : 4.154 17.721 666 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.00 % Allowed : 24.82 % Favored : 70.18 % 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: 2.04 (0.35), residues: 606 helix: 1.98 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.41 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.020 0.001 PHE B 23 TYR 0.012 0.001 TYR B 33 ARG 0.005 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 121 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 TRP cc_start: 0.7407 (t-100) cc_final: 0.6716 (m-90) REVERT: A 312 PHE cc_start: 0.8235 (m-10) cc_final: 0.7841 (m-10) REVERT: B 34 ARG cc_start: 0.7033 (mtm180) cc_final: 0.6227 (mpp80) REVERT: B 127 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7398 (t80) REVERT: B 210 TRP cc_start: 0.7706 (t-100) cc_final: 0.7069 (m-90) outliers start: 28 outliers final: 14 residues processed: 112 average time/residue: 0.2194 time to fit residues: 31.7489 Evaluate side-chains 101 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE 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 326 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 ASN 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 294 PHE Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.260993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.239943 restraints weight = 7723.087| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 1.87 r_work: 0.4556 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5314 Z= 0.238 Angle : 0.696 11.650 7176 Z= 0.350 Chirality : 0.041 0.164 764 Planarity : 0.004 0.055 892 Dihedral : 4.289 16.972 666 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.00 % Allowed : 24.11 % Favored : 70.89 % 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: 1.86 (0.34), residues: 606 helix: 1.85 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.42 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 16 HIS 0.003 0.000 HIS A 283 PHE 0.015 0.001 PHE A 23 TYR 0.010 0.001 TYR A 239 ARG 0.006 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 117 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: A 210 TRP cc_start: 0.7416 (t-100) cc_final: 0.6670 (m-90) REVERT: A 312 PHE cc_start: 0.8218 (m-10) cc_final: 0.7788 (m-10) REVERT: B 127 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 203 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7751 (tp) REVERT: B 210 TRP cc_start: 0.7697 (t-100) cc_final: 0.7128 (m-90) outliers start: 28 outliers final: 17 residues processed: 109 average time/residue: 0.2165 time to fit residues: 31.3261 Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 194 VAL 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 309 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 ASN 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 294 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.260830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.240149 restraints weight = 7691.387| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 1.78 r_work: 0.4551 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5314 Z= 0.228 Angle : 0.694 10.248 7176 Z= 0.351 Chirality : 0.040 0.168 764 Planarity : 0.004 0.061 892 Dihedral : 4.256 17.238 666 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.75 % Allowed : 24.82 % Favored : 71.43 % 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: 1.89 (0.35), residues: 606 helix: 1.86 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -2.31 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 16 HIS 0.002 0.001 HIS B 283 PHE 0.017 0.001 PHE A 23 TYR 0.011 0.001 TYR A 239 ARG 0.005 0.001 ARG A 90 *********************** 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 109 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: A 304 GLU cc_start: 0.8180 (mp0) cc_final: 0.7854 (mp0) REVERT: A 312 PHE cc_start: 0.8188 (m-10) cc_final: 0.7979 (m-10) REVERT: B 127 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7391 (t80) REVERT: B 203 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7723 (tp) REVERT: B 210 TRP cc_start: 0.7681 (t-100) cc_final: 0.7118 (m-90) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.1811 time to fit residues: 23.9835 Evaluate side-chains 101 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 194 VAL 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 326 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 294 PHE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.262583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.242321 restraints weight = 7734.477| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 1.79 r_work: 0.4581 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.6865 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= 0.187 Angle : 0.677 10.119 7176 Z= 0.341 Chirality : 0.039 0.156 764 Planarity : 0.004 0.063 892 Dihedral : 4.118 16.247 666 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.04 % Allowed : 26.07 % Favored : 70.89 % 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: 2.13 (0.35), residues: 606 helix: 2.01 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.26 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 16 HIS 0.002 0.000 HIS A 283 PHE 0.017 0.001 PHE B 23 TYR 0.010 0.001 TYR B 33 ARG 0.002 0.000 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 102 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: A 312 PHE cc_start: 0.8170 (m-10) cc_final: 0.7918 (m-10) REVERT: B 127 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7380 (t80) REVERT: B 203 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7671 (tp) REVERT: B 210 TRP cc_start: 0.7563 (t-100) cc_final: 0.7028 (m-90) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.1757 time to fit residues: 21.7690 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE 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 309 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 107 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 294 PHE 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 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 B 91 GLN B 115 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.259569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.239702 restraints weight = 7802.114| |-----------------------------------------------------------------------------| r_work (start): 0.4633 rms_B_bonded: 1.81 r_work: 0.4555 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5314 Z= 0.239 Angle : 0.729 9.136 7176 Z= 0.368 Chirality : 0.041 0.168 764 Planarity : 0.005 0.064 892 Dihedral : 4.228 17.531 666 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.04 % Allowed : 26.96 % Favored : 70.00 % 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: 1.88 (0.34), residues: 606 helix: 1.81 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.11 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 16 HIS 0.003 0.001 HIS A 283 PHE 0.021 0.001 PHE B 23 TYR 0.010 0.001 TYR A 239 ARG 0.004 0.001 ARG A 90 ********************** 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 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7771 (tp) cc_final: 0.7186 (mp) REVERT: B 127 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7512 (t80) REVERT: B 203 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7755 (tp) REVERT: B 210 TRP cc_start: 0.7690 (t-100) cc_final: 0.7188 (m-90) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.1855 time to fit residues: 22.0495 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 CYS 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 326 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 107 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 294 PHE 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 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.264021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.245428 restraints weight = 7590.776| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 1.85 r_work: 0.4569 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5314 Z= 0.206 Angle : 0.706 9.851 7176 Z= 0.355 Chirality : 0.039 0.169 764 Planarity : 0.004 0.065 892 Dihedral : 4.130 16.558 666 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.86 % Allowed : 26.96 % Favored : 70.18 % 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: 2.02 (0.35), residues: 606 helix: 1.91 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.12 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 16 HIS 0.002 0.000 HIS B 283 PHE 0.019 0.001 PHE A 23 TYR 0.009 0.001 TYR A 239 ARG 0.002 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.77 seconds wall clock time: 55 minutes 2.60 seconds (3302.60 seconds total)