Starting phenix.real_space_refine on Fri Aug 22 12:40:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlx_36407/08_2025/8jlx_36407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlx_36407/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jlx_36407/08_2025/8jlx_36407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlx_36407/08_2025/8jlx_36407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jlx_36407/08_2025/8jlx_36407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlx_36407/08_2025/8jlx_36407.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.87, per 1000 atoms: 0.38 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: 0.18 Conformation dependent library (CDL) restraints added in 92.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.11 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: 0.33 Time building geometry restraints manager: 0.26 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: 3.740 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.680 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- 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 : 12.50 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG H 13 TYR 0.015 0.002 TYR A1358 PHE 0.005 0.001 PHE L 87 TRP 0.009 0.002 TRP A1199 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2334) covalent geometry : angle 0.74635 ( 3173) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.73061 ( 16) hydrogen bonds : bond 0.16599 ( 79) hydrogen bonds : angle 7.43311 ( 198) *********************** 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 : 0.095 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: 0.5093 time to fit residues: 30.2474 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 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 = 35)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.167490 restraints weight = 2959.342| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.88 r_work: 0.3840 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 10.23 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A1192 TYR 0.019 0.002 TYR A1358 PHE 0.005 0.001 PHE L 87 TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 2334) covalent geometry : angle 0.75235 ( 3173) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.62067 ( 16) hydrogen bonds : bond 0.04114 ( 79) hydrogen bonds : angle 5.84332 ( 198) *********************** 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 : 0.101 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.7313 (mt0) cc_final: 0.7040 (mt0) REVERT: L 38 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7528 (tt0) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 0.4826 time to fit residues: 27.7448 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 : 0.089 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.187559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.172478 restraints weight = 2957.869| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.81 r_work: 0.3868 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2342 Z= 0.144 Angle : 0.675 7.132 3189 Z= 0.353 Chirality : 0.046 0.174 340 Planarity : 0.005 0.048 402 Dihedral : 5.384 20.680 319 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 5.10 % Allowed : 19.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.59 (0.42), residues: 146 loop : -1.98 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 13 TYR 0.014 0.002 TYR A1358 PHE 0.004 0.001 PHE L 87 TRP 0.008 0.001 TRP A1199 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2334) covalent geometry : angle 0.67158 ( 3173) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.20496 ( 16) hydrogen bonds : bond 0.03454 ( 79) hydrogen bonds : angle 5.44520 ( 198) *********************** 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: 13 poor density : 50 time to evaluate : 0.123 Fit side-chains REVERT: H 60 CYS cc_start: 0.8620 (p) cc_final: 0.8396 (p) REVERT: H 82 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7433 (mm-30) REVERT: L 38 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7538 (tt0) outliers start: 13 outliers final: 5 residues processed: 58 average time/residue: 0.4329 time to fit residues: 25.8248 Evaluate side-chains 50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 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 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 = 0.4079 r_free = 0.4079 target = 0.182884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167164 restraints weight = 2938.285| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.93 r_work: 0.3848 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2342 Z= 0.174 Angle : 0.703 7.229 3189 Z= 0.368 Chirality : 0.048 0.220 340 Planarity : 0.005 0.048 402 Dihedral : 5.534 20.372 319 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 6.67 % Allowed : 18.04 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.65 (0.42), residues: 140 loop : -1.97 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 13 TYR 0.016 0.002 TYR A1358 PHE 0.006 0.001 PHE L 87 TRP 0.010 0.002 TRP H 36 HIS 0.001 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2334) covalent geometry : angle 0.69908 ( 3173) SS BOND : bond 0.00339 ( 8) SS BOND : angle 1.21479 ( 16) hydrogen bonds : bond 0.03543 ( 79) hydrogen bonds : angle 5.46298 ( 198) *********************** 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 65 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.095 Fit side-chains REVERT: L 38 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7604 (tt0) outliers start: 17 outliers final: 8 residues processed: 60 average time/residue: 0.4541 time to fit residues: 28.0029 Evaluate side-chains 52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.181822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166606 restraints weight = 2867.651| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.84 r_work: 0.3823 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2342 Z= 0.228 Angle : 0.773 7.367 3189 Z= 0.402 Chirality : 0.050 0.187 340 Planarity : 0.005 0.044 402 Dihedral : 5.908 21.141 319 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 6.67 % Allowed : 20.39 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.87 (0.42), residues: 146 loop : -2.12 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG H 13 TYR 0.019 0.003 TYR A1358 PHE 0.007 0.001 PHE L 87 TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 2334) covalent geometry : angle 0.76885 ( 3173) SS BOND : bond 0.00402 ( 8) SS BOND : angle 1.32154 ( 16) hydrogen bonds : bond 0.03775 ( 79) hydrogen bonds : angle 5.63919 ( 198) *********************** 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: 17 poor density : 44 time to evaluate : 0.093 Fit side-chains REVERT: L 38 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7590 (tt0) outliers start: 17 outliers final: 11 residues processed: 55 average time/residue: 0.4309 time to fit residues: 24.3812 Evaluate side-chains 54 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.064 ------------------------------------------------------------------------------- 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 111 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 1 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN 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 = 0.4128 r_free = 0.4128 target = 0.187086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172009 restraints weight = 2847.311| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.87 r_work: 0.3880 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1913 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= 0.125 Angle : 0.664 7.173 3189 Z= 0.346 Chirality : 0.045 0.165 340 Planarity : 0.005 0.043 402 Dihedral : 5.243 20.719 319 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.49 % Allowed : 22.35 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.68 (0.42), residues: 145 loop : -1.99 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1192 TYR 0.013 0.002 TYR A1358 PHE 0.004 0.001 PHE L 87 TRP 0.009 0.001 TRP A1199 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2334) covalent geometry : angle 0.66184 ( 3173) SS BOND : bond 0.00282 ( 8) SS BOND : angle 0.98378 ( 16) hydrogen bonds : bond 0.03131 ( 79) hydrogen bonds : angle 5.24864 ( 198) *********************** 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 61 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.090 Fit side-chains REVERT: L 38 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7514 (tt0) outliers start: 14 outliers final: 6 residues processed: 60 average time/residue: 0.3718 time to fit residues: 23.0012 Evaluate side-chains 48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 15 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.0030 chunk 20 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.185784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170972 restraints weight = 2883.839| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.82 r_work: 0.3863 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2023 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= 0.175 Angle : 0.725 7.156 3189 Z= 0.383 Chirality : 0.048 0.270 340 Planarity : 0.005 0.047 402 Dihedral : 5.533 20.930 319 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 7.45 % Allowed : 22.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.73 (0.42), residues: 140 loop : -2.14 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1192 TYR 0.015 0.002 TYR A1358 PHE 0.004 0.001 PHE L 87 TRP 0.009 0.002 TRP A1199 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 2334) covalent geometry : angle 0.72022 ( 3173) SS BOND : bond 0.00265 ( 8) SS BOND : angle 1.38961 ( 16) hydrogen bonds : bond 0.03338 ( 79) hydrogen bonds : angle 5.27413 ( 198) *********************** 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 61 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.099 Fit side-chains REVERT: L 38 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7537 (tt0) outliers start: 19 outliers final: 9 residues processed: 57 average time/residue: 0.3612 time to fit residues: 21.2769 Evaluate side-chains 51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.185359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.170465 restraints weight = 2804.936| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.82 r_work: 0.3863 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2342 Z= 0.165 Angle : 0.717 7.490 3189 Z= 0.377 Chirality : 0.047 0.234 340 Planarity : 0.005 0.053 402 Dihedral : 5.521 20.791 319 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.88 % Allowed : 23.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.48), residues: 285 helix: None (None), residues: 0 sheet: -0.76 (0.42), residues: 145 loop : -2.17 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1192 TYR 0.015 0.002 TYR A1358 PHE 0.005 0.001 PHE L 87 TRP 0.010 0.002 TRP H 36 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2334) covalent geometry : angle 0.71286 ( 3173) SS BOND : bond 0.00311 ( 8) SS BOND : angle 1.29350 ( 16) hydrogen bonds : bond 0.03288 ( 79) hydrogen bonds : angle 5.26003 ( 198) *********************** 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 57 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.109 Fit side-chains REVERT: A 1192 ARG cc_start: 0.6268 (ttp-110) cc_final: 0.6051 (mtp85) REVERT: L 38 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7503 (tt0) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.2948 time to fit residues: 15.8357 Evaluate side-chains 51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.053 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 6 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170776 restraints weight = 2922.749| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.81 r_work: 0.3863 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2088 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= 0.170 Angle : 0.737 8.184 3189 Z= 0.381 Chirality : 0.047 0.220 340 Planarity : 0.005 0.046 402 Dihedral : 5.567 20.189 319 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 6.67 % Allowed : 23.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.70 (0.42), residues: 144 loop : -2.16 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1192 TYR 0.015 0.002 TYR A1358 PHE 0.005 0.001 PHE L 87 TRP 0.009 0.002 TRP H 36 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2334) covalent geometry : angle 0.73341 ( 3173) SS BOND : bond 0.00295 ( 8) SS BOND : angle 1.28212 ( 16) hydrogen bonds : bond 0.03241 ( 79) hydrogen bonds : angle 5.28072 ( 198) *********************** 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 58 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.056 Fit side-chains REVERT: A 1192 ARG cc_start: 0.6243 (ttp-110) cc_final: 0.6029 (mtp85) REVERT: L 38 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7507 (tt0) outliers start: 17 outliers final: 11 residues processed: 54 average time/residue: 0.3171 time to fit residues: 17.6689 Evaluate side-chains 51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 1 ASP 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 18 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.183367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168725 restraints weight = 2930.222| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.82 r_work: 0.3851 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2342 Z= 0.199 Angle : 0.763 7.509 3189 Z= 0.397 Chirality : 0.049 0.227 340 Planarity : 0.005 0.044 402 Dihedral : 5.740 20.277 319 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.49 % Allowed : 25.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.76 (0.43), residues: 139 loop : -2.22 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1192 TYR 0.016 0.002 TYR A1358 PHE 0.005 0.001 PHE L 87 TRP 0.012 0.002 TRP A1185 HIS 0.001 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 2334) covalent geometry : angle 0.75839 ( 3173) SS BOND : bond 0.00333 ( 8) SS BOND : angle 1.39208 ( 16) hydrogen bonds : bond 0.03370 ( 79) hydrogen bonds : angle 5.38603 ( 198) ********************** 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 55 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.069 Fit side-chains REVERT: A 1192 ARG cc_start: 0.6312 (ttp-110) cc_final: 0.6087 (mtp85) REVERT: L 38 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7595 (tt0) outliers start: 14 outliers final: 12 residues processed: 51 average time/residue: 0.3638 time to fit residues: 19.1746 Evaluate side-chains 54 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 1 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 34 ASN 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 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.0050 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.183598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.168610 restraints weight = 2941.230| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.88 r_work: 0.3843 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2163 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= 0.187 Angle : 0.747 7.517 3189 Z= 0.390 Chirality : 0.048 0.213 340 Planarity : 0.005 0.041 402 Dihedral : 5.723 20.394 319 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 5.49 % Allowed : 25.88 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.49), residues: 285 helix: None (None), residues: 0 sheet: -0.82 (0.43), residues: 140 loop : -2.19 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1192 TYR 0.015 0.002 TYR A1358 PHE 0.005 0.001 PHE L 87 TRP 0.013 0.002 TRP A1185 HIS 0.001 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 2334) covalent geometry : angle 0.74268 ( 3173) SS BOND : bond 0.00317 ( 8) SS BOND : angle 1.36367 ( 16) hydrogen bonds : bond 0.03303 ( 79) hydrogen bonds : angle 5.41771 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.84 seconds wall clock time: 21 minutes 17.15 seconds (1277.15 seconds total)