Starting phenix.real_space_refine on Fri May 9 14:01:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlx_36407/05_2025/8jlx_36407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlx_36407/05_2025/8jlx_36407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlx_36407/05_2025/8jlx_36407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlx_36407/05_2025/8jlx_36407.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlx_36407/05_2025/8jlx_36407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlx_36407/05_2025/8jlx_36407.cif" } resolution = 3.0 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= -0.000 sd= 0.051 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 22 5.16 5 C 1417 2.51 5 N 382 2.21 5 O 456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2277 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 539 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain breaks: 1 Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 907 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 2.52, per 1000 atoms: 1.11 Number of scatterers: 2277 At special positions: 0 Unit cell: (52.25, 69.35, 89.3, 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 22 16.00 O 456 8.00 N 382 7.00 C 1417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1198 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1205 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1207 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1180 " distance=2.03 Simple disulfide: pdb=" SG CYS A1193 " - pdb=" SG CYS A1360 " distance=2.03 Simple disulfide: pdb=" SG CYS A1208 " - pdb=" SG CYS A1368 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 0.49 Conformation dependent library (CDL) restraints added in 261.6 milliseconds 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 532 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.8% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.711A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.703A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1162 through 1164 Processing sheet with id=AA2, first strand: chain 'A' and resid 1356 through 1359 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.071A pdb=" N ALA H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 50 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.737A pdb=" N CYS H 96 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP H 107 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASN H 98 " --> pdb=" O ASP H 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.450A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 198 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: 0.54 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 723 1.34 - 1.46: 629 1.46 - 1.58: 955 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 2334 Sorted by residual: bond pdb=" CB CYS A1207 " pdb=" SG CYS A1207 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CB CYS A1368 " pdb=" SG CYS A1368 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.58e-01 bond pdb=" C THR L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.352 -0.019 2.34e-02 1.83e+03 6.32e-01 bond pdb=" CG GLU H 82 " pdb=" CD GLU H 82 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 5.82e-01 bond pdb=" CB CYS A1208 " pdb=" SG CYS A1208 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.32e-01 ... (remaining 2329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 2922 1.23 - 2.45: 204 2.45 - 3.68: 29 3.68 - 4.90: 14 4.90 - 6.13: 4 Bond angle restraints: 3173 Sorted by residual: angle pdb=" N THR L 7 " pdb=" CA THR L 7 " pdb=" C THR L 7 " ideal model delta sigma weight residual 109.81 115.61 -5.80 2.21e+00 2.05e-01 6.90e+00 angle pdb=" C ASP A1364 " pdb=" N TRP A1365 " pdb=" CA TRP A1365 " ideal model delta sigma weight residual 121.80 127.09 -5.29 2.44e+00 1.68e-01 4.70e+00 angle pdb=" CA THR L 7 " pdb=" C THR L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 118.44 121.84 -3.40 1.59e+00 3.96e-01 4.56e+00 angle pdb=" N PRO H 14 " pdb=" CA PRO H 14 " pdb=" C PRO H 14 " ideal model delta sigma weight residual 110.50 113.83 -3.33 1.57e+00 4.06e-01 4.49e+00 angle pdb=" CA CYS A1368 " pdb=" CB CYS A1368 " pdb=" SG CYS A1368 " ideal model delta sigma weight residual 114.40 119.26 -4.86 2.30e+00 1.89e-01 4.47e+00 ... (remaining 3168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 1233 16.88 - 33.76: 107 33.76 - 50.63: 24 50.63 - 67.51: 4 67.51 - 84.38: 8 Dihedral angle restraints: 1376 sinusoidal: 537 harmonic: 839 Sorted by residual: dihedral pdb=" CB CYS A1175 " pdb=" SG CYS A1175 " pdb=" SG CYS A1180 " pdb=" CB CYS A1180 " ideal model delta sinusoidal sigma weight residual -86.00 -15.17 -70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A1208 " pdb=" SG CYS A1208 " pdb=" SG CYS A1368 " pdb=" CB CYS A1368 " ideal model delta sinusoidal sigma weight residual 93.00 162.79 -69.79 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS A1169 " pdb=" SG CYS A1169 " pdb=" SG CYS A1205 " pdb=" CB CYS A1205 " ideal model delta sinusoidal sigma weight residual 93.00 41.08 51.92 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 1373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 243 0.045 - 0.091: 68 0.091 - 0.136: 25 0.136 - 0.182: 2 0.182 - 0.227: 2 Chirality restraints: 340 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA THR L 7 " pdb=" N THR L 7 " pdb=" C THR L 7 " pdb=" CB THR L 7 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 337 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 7 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO L 8 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO L 59 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A1160 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A1161 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A1161 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1161 " -0.017 5.00e-02 4.00e+02 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 442 2.78 - 3.31: 2014 3.31 - 3.84: 3555 3.84 - 4.37: 4331 4.37 - 4.90: 7602 Nonbonded interactions: 17944 Sorted by model distance: nonbonded pdb=" NE2 GLN H 6 " pdb=" O TYR H 94 " model vdw 2.247 3.120 nonbonded pdb=" O VAL H 50 " pdb=" OG1 THR H 58 " model vdw 2.258 3.040 nonbonded pdb=" NE1 TRP A1197 " pdb=" OD2 ASP H 31 " model vdw 2.302 3.120 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.308 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.320 3.040 ... (remaining 17939 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.660 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 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:10.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2342 Z= 0.193 Angle : 0.755 6.127 3189 Z= 0.400 Chirality : 0.050 0.227 340 Planarity : 0.005 0.057 402 Dihedral : 14.315 84.384 820 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.27 (0.47), residues: 285 helix: None (None), residues: 0 sheet: -0.85 (0.42), residues: 141 loop : -2.20 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1199 HIS 0.002 0.001 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.015 0.002 TYR A1358 ARG 0.004 0.001 ARG H 13 Details of bonding type rmsd hydrogen bonds : bond 0.16599 ( 79) hydrogen bonds : angle 7.43311 ( 198) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.73061 ( 16) covalent geometry : bond 0.00429 ( 2334) covalent geometry : angle 0.74635 ( 3173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.6809 (mt0) cc_final: 0.6563 (mt0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.9929 time to fit residues: 59.0837 Evaluate side-chains 41 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 GLN L 6 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.183173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167586 restraints weight = 2917.153| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.85 r_work: 0.3841 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2342 Z= 0.213 Angle : 0.759 6.886 3189 Z= 0.399 Chirality : 0.050 0.199 340 Planarity : 0.006 0.060 402 Dihedral : 5.832 21.841 319 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 5.88 % Allowed : 14.90 % Favored : 79.22 % 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: -2.12 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.81 (0.41), residues: 149 loop : -2.08 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.019 0.002 TYR A1358 ARG 0.008 0.001 ARG A1192 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 79) hydrogen bonds : angle 5.84332 ( 198) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.62067 ( 16) covalent geometry : bond 0.00482 ( 2334) covalent geometry : angle 0.75235 ( 3173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.7312 (mt0) cc_final: 0.7038 (mt0) REVERT: L 38 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7528 (tt0) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 0.9318 time to fit residues: 53.5740 Evaluate side-chains 48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.185128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169810 restraints weight = 2883.944| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.85 r_work: 0.3854 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2342 Z= 0.172 Angle : 0.708 7.243 3189 Z= 0.370 Chirality : 0.047 0.180 340 Planarity : 0.005 0.053 402 Dihedral : 5.602 21.034 319 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.88 % Allowed : 18.43 % Favored : 75.69 % 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: -1.98 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.66 (0.42), residues: 146 loop : -2.03 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.001 0.000 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.016 0.002 TYR A1358 ARG 0.009 0.001 ARG H 13 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 79) hydrogen bonds : angle 5.57078 ( 198) SS BOND : bond 0.00338 ( 8) SS BOND : angle 1.31108 ( 16) covalent geometry : bond 0.00387 ( 2334) covalent geometry : angle 0.70340 ( 3173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.7315 (mt0) cc_final: 0.7041 (mt0) REVERT: H 82 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7521 (mm-30) REVERT: L 38 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: L 89 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7491 (tt0) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 0.8875 time to fit residues: 52.9392 Evaluate side-chains 51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN H 109 GLN L 3 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166207 restraints weight = 2910.755| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.93 r_work: 0.3857 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2342 Z= 0.148 Angle : 0.675 7.234 3189 Z= 0.353 Chirality : 0.046 0.172 340 Planarity : 0.005 0.043 402 Dihedral : 5.407 20.569 319 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 7.06 % Allowed : 18.82 % Favored : 74.12 % 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 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.65 (0.42), residues: 146 loop : -2.01 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1199 HIS 0.001 0.000 HIS L 55 PHE 0.004 0.001 PHE L 87 TYR 0.014 0.002 TYR A1358 ARG 0.009 0.001 ARG H 13 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 79) hydrogen bonds : angle 5.38413 ( 198) SS BOND : bond 0.00317 ( 8) SS BOND : angle 1.14290 ( 16) covalent geometry : bond 0.00335 ( 2334) covalent geometry : angle 0.67151 ( 3173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7640 (tt0) outliers start: 18 outliers final: 9 residues processed: 61 average time/residue: 0.8720 time to fit residues: 54.7365 Evaluate side-chains 52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 GLN L 3 GLN L 34 ASN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.181020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165476 restraints weight = 2916.150| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.89 r_work: 0.3833 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2342 Z= 0.190 Angle : 0.735 7.239 3189 Z= 0.381 Chirality : 0.049 0.234 340 Planarity : 0.005 0.049 402 Dihedral : 5.636 20.648 319 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.27 % Allowed : 19.61 % Favored : 74.12 % 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: -2.14 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.78 (0.42), residues: 146 loop : -2.12 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.001 0.001 HIS L 55 PHE 0.006 0.001 PHE L 87 TYR 0.017 0.002 TYR A1358 ARG 0.010 0.002 ARG H 13 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 79) hydrogen bonds : angle 5.46939 ( 198) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.19558 ( 16) covalent geometry : bond 0.00428 ( 2334) covalent geometry : angle 0.73215 ( 3173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7565 (tt0) outliers start: 16 outliers final: 9 residues processed: 57 average time/residue: 0.8441 time to fit residues: 49.7619 Evaluate side-chains 52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166105 restraints weight = 2888.687| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.87 r_work: 0.3847 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2342 Z= 0.180 Angle : 0.742 7.300 3189 Z= 0.389 Chirality : 0.047 0.186 340 Planarity : 0.005 0.044 402 Dihedral : 5.579 21.103 319 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 7.06 % Allowed : 21.96 % Favored : 70.98 % 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: -2.21 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.76 (0.42), residues: 140 loop : -2.21 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.001 0.001 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.016 0.002 TYR A1358 ARG 0.011 0.001 ARG H 13 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 79) hydrogen bonds : angle 5.47190 ( 198) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.15231 ( 16) covalent geometry : bond 0.00408 ( 2334) covalent geometry : angle 0.73922 ( 3173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7577 (tt0) outliers start: 18 outliers final: 9 residues processed: 59 average time/residue: 0.7412 time to fit residues: 45.2463 Evaluate side-chains 52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.185057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169921 restraints weight = 2901.535| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.87 r_work: 0.3856 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2342 Z= 0.163 Angle : 0.718 7.186 3189 Z= 0.377 Chirality : 0.047 0.171 340 Planarity : 0.005 0.049 402 Dihedral : 5.533 22.003 319 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 6.27 % Allowed : 23.53 % Favored : 70.20 % 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: -2.18 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.74 (0.43), residues: 140 loop : -2.19 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1199 HIS 0.001 0.000 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.015 0.002 TYR A1358 ARG 0.013 0.001 ARG H 13 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 79) hydrogen bonds : angle 5.33792 ( 198) SS BOND : bond 0.00280 ( 8) SS BOND : angle 1.37302 ( 16) covalent geometry : bond 0.00374 ( 2334) covalent geometry : angle 0.71288 ( 3173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7535 (tt0) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 0.7401 time to fit residues: 42.8635 Evaluate side-chains 50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 0.0020 chunk 11 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171040 restraints weight = 2947.897| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.92 r_work: 0.3866 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2342 Z= 0.137 Angle : 0.688 7.467 3189 Z= 0.360 Chirality : 0.045 0.173 340 Planarity : 0.005 0.055 402 Dihedral : 5.330 20.794 319 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.49 % Allowed : 24.31 % Favored : 70.20 % 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: -2.10 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.68 (0.43), residues: 140 loop : -2.14 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1199 HIS 0.000 0.000 HIS L 55 PHE 0.005 0.001 PHE L 87 TYR 0.013 0.002 TYR L 86 ARG 0.014 0.002 ARG H 13 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 79) hydrogen bonds : angle 5.17255 ( 198) SS BOND : bond 0.00297 ( 8) SS BOND : angle 1.12409 ( 16) covalent geometry : bond 0.00314 ( 2334) covalent geometry : angle 0.68520 ( 3173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 1192 ARG cc_start: 0.6252 (ttp-110) cc_final: 0.6021 (mtp85) REVERT: L 38 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7522 (tt0) outliers start: 14 outliers final: 9 residues processed: 54 average time/residue: 0.7245 time to fit residues: 40.5388 Evaluate side-chains 50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.0040 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.185825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.170787 restraints weight = 2822.609| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.85 r_work: 0.3878 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2342 Z= 0.151 Angle : 0.697 7.354 3189 Z= 0.365 Chirality : 0.048 0.323 340 Planarity : 0.005 0.047 402 Dihedral : 5.381 19.837 319 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 5.49 % Allowed : 24.31 % Favored : 70.20 % 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: -2.10 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.69 (0.43), residues: 140 loop : -2.13 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1199 HIS 0.001 0.000 HIS L 55 PHE 0.004 0.001 PHE L 87 TYR 0.013 0.002 TYR A1358 ARG 0.011 0.001 ARG A1192 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 79) hydrogen bonds : angle 5.10665 ( 198) SS BOND : bond 0.00299 ( 8) SS BOND : angle 1.13488 ( 16) covalent geometry : bond 0.00349 ( 2334) covalent geometry : angle 0.69407 ( 3173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 1192 ARG cc_start: 0.6238 (ttp-110) cc_final: 0.5999 (mtp85) REVERT: L 38 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7540 (tt0) outliers start: 14 outliers final: 10 residues processed: 54 average time/residue: 0.7026 time to fit residues: 39.3666 Evaluate side-chains 52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.186328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.171214 restraints weight = 2887.042| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.88 r_work: 0.3877 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2342 Z= 0.143 Angle : 0.690 7.406 3189 Z= 0.361 Chirality : 0.047 0.281 340 Planarity : 0.005 0.044 402 Dihedral : 5.314 19.528 319 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.71 % Allowed : 25.49 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.70 (0.42), residues: 145 loop : -2.10 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1199 HIS 0.001 0.000 HIS H 41 PHE 0.004 0.001 PHE L 87 TYR 0.013 0.002 TYR L 86 ARG 0.011 0.001 ARG A1192 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 79) hydrogen bonds : angle 5.09401 ( 198) SS BOND : bond 0.00280 ( 8) SS BOND : angle 1.09662 ( 16) covalent geometry : bond 0.00330 ( 2334) covalent geometry : angle 0.68742 ( 3173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 1192 ARG cc_start: 0.6231 (ttp-110) cc_final: 0.6001 (mtp85) REVERT: L 38 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7535 (tt0) outliers start: 12 outliers final: 11 residues processed: 54 average time/residue: 0.6820 time to fit residues: 38.1877 Evaluate side-chains 55 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1371 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.185802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.170822 restraints weight = 2864.144| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.85 r_work: 0.3854 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2342 Z= 0.157 Angle : 0.702 7.386 3189 Z= 0.367 Chirality : 0.047 0.271 340 Planarity : 0.005 0.042 402 Dihedral : 5.406 19.033 319 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.71 % Allowed : 25.88 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.71 (0.42), residues: 140 loop : -2.16 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1185 HIS 0.001 0.000 HIS L 55 PHE 0.004 0.001 PHE L 87 TYR 0.014 0.002 TYR A1358 ARG 0.010 0.001 ARG A1192 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 79) hydrogen bonds : angle 5.18278 ( 198) SS BOND : bond 0.00301 ( 8) SS BOND : angle 1.16787 ( 16) covalent geometry : bond 0.00363 ( 2334) covalent geometry : angle 0.69890 ( 3173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.90 seconds wall clock time: 40 minutes 56.49 seconds (2456.49 seconds total)