Starting phenix.real_space_refine on Thu Sep 10 20:29:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7exa_31367/09_2026/7exa_31367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7exa_31367/09_2026/7exa_31367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7exa_31367/09_2026/7exa_31367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7exa_31367/09_2026/7exa_31367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7exa_31367/09_2026/7exa_31367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7exa_31367/09_2026/7exa_31367.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.007 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 19 5.16 5 C 1942 2.51 5 N 530 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3088 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2968 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 0.83, per 1000 atoms: 0.27 Number of scatterers: 3088 At special positions: 0 Unit cell: (91.74, 66.66, 79.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 6 15.00 O 591 8.00 N 530 7.00 C 1942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 90.0 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 69.5% alpha, 3.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.289A pdb=" N LEU A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.553A pdb=" N GLY A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 179 removed outlier: 3.582A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 4.202A pdb=" N ASP A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.639A pdb=" N SER A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.655A pdb=" N MET A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.770A pdb=" N GLY A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 325 through 328 Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.653A pdb=" N VAL A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 358 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.275A pdb=" N VAL A 35 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N CYS A 102 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 37 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 39 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY A 106 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 115 " --> pdb=" O ASP A 105 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.40 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 697 1.33 - 1.45: 697 1.45 - 1.57: 1725 1.57 - 1.69: 11 1.69 - 1.81: 31 Bond restraints: 3161 Sorted by residual: bond pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 bond pdb=" N GLN A 187 " pdb=" CA GLN A 187 " ideal model delta sigma weight residual 1.455 1.489 -0.034 9.60e-03 1.09e+04 1.25e+01 bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.462 1.496 -0.035 1.01e-02 9.80e+03 1.18e+01 bond pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.99e+00 bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.56e+00 ... (remaining 3156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 3695 1.77 - 3.53: 545 3.53 - 5.30: 54 5.30 - 7.07: 3 7.07 - 8.83: 7 Bond angle restraints: 4304 Sorted by residual: angle pdb=" C3' U B 20 " pdb=" C2' U B 20 " pdb=" C1' U B 20 " ideal model delta sigma weight residual 101.30 104.65 -3.35 7.00e-01 2.04e+00 2.29e+01 angle pdb=" C3' U B 24 " pdb=" C2' U B 24 " pdb=" C1' U B 24 " ideal model delta sigma weight residual 101.30 104.62 -3.32 7.00e-01 2.04e+00 2.25e+01 angle pdb=" C3' U B 23 " pdb=" C2' U B 23 " pdb=" C1' U B 23 " ideal model delta sigma weight residual 101.30 104.61 -3.31 7.00e-01 2.04e+00 2.23e+01 angle pdb=" C3' U B 21 " pdb=" C2' U B 21 " pdb=" C1' U B 21 " ideal model delta sigma weight residual 101.30 104.55 -3.25 7.00e-01 2.04e+00 2.16e+01 angle pdb=" C4' U B 23 " pdb=" C3' U B 23 " pdb=" O3' U B 23 " ideal model delta sigma weight residual 113.00 121.83 -8.83 2.00e+00 2.50e-01 1.95e+01 ... (remaining 4299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 1688 17.89 - 35.79: 185 35.79 - 53.68: 40 53.68 - 71.58: 13 71.58 - 89.47: 5 Dihedral angle restraints: 1931 sinusoidal: 839 harmonic: 1092 Sorted by residual: dihedral pdb=" C5' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" O3' U B 25 " ideal model delta sinusoidal sigma weight residual 147.00 106.23 40.77 1 8.00e+00 1.56e-02 3.64e+01 dihedral pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " pdb=" C1' U B 25 " ideal model delta sinusoidal sigma weight residual -35.00 0.49 -35.49 1 8.00e+00 1.56e-02 2.79e+01 dihedral pdb=" O4' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " ideal model delta sinusoidal sigma weight residual 24.00 -11.43 35.43 1 8.00e+00 1.56e-02 2.78e+01 ... (remaining 1928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 292 0.052 - 0.105: 122 0.105 - 0.157: 39 0.157 - 0.209: 15 0.209 - 0.261: 12 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA LEU A 90 " pdb=" N LEU A 90 " pdb=" C LEU A 90 " pdb=" CB LEU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C3' U B 23 " pdb=" C4' U B 23 " pdb=" O3' U B 23 " pdb=" C2' U B 23 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 477 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 277 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C LEU A 277 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU A 277 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 278 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 24 " -0.020 2.00e-02 2.50e+03 1.21e-02 3.30e+00 pdb=" N1 U B 24 " 0.030 2.00e-02 2.50e+03 pdb=" C2 U B 24 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U B 24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 314 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C ALA A 314 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 314 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 315 " -0.010 2.00e-02 2.50e+03 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 16 2.57 - 3.15: 2400 3.15 - 3.73: 4705 3.73 - 4.32: 6964 4.32 - 4.90: 11041 Nonbonded interactions: 25126 Sorted by model distance: nonbonded pdb=" O LYS A 180 " pdb=" O ALA A 184 " model vdw 1.984 3.040 nonbonded pdb=" OG SER A 94 " pdb=" OE1 GLN A 231 " model vdw 2.252 3.040 nonbonded pdb=" O SER A 61 " pdb=" NH2 ARG A 69 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN A 63 " pdb=" OD2 ASP A 136 " model vdw 2.385 3.040 nonbonded pdb=" O ALA A 64 " pdb=" NH1 ARG A 69 " model vdw 2.394 3.120 ... (remaining 25121 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: 12.190 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.320 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.010 0.042 3161 Z= 0.694 Angle : 1.227 8.833 4304 Z= 0.897 Chirality : 0.075 0.261 480 Planarity : 0.005 0.030 543 Dihedral : 16.181 89.470 1233 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 9.94 % Favored : 88.46 % 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 are not related in a simple way. whole: -0.45 (0.40), residues: 372 helix: -0.46 (0.31), residues: 223 sheet: 0.89 (1.43), residues: 14 loop : 0.20 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 10 TYR 0.022 0.003 TYR A 361 PHE 0.016 0.003 PHE A 289 TRP 0.011 0.002 TRP A 175 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.01040 / 0.69 ( 3161) covalent geometry : angle 1.22651 / 0.90 ( 4304) hydrogen bonds : bond 0.18406 / 11.63 ( 167) hydrogen bonds : angle 6.19003 / 4.44 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.118 Fit side-chains REVERT: A 6 LYS cc_start: 0.8325 (mttt) cc_final: 0.8024 (mttp) REVERT: A 65 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7552 (mtp180) REVERT: A 88 ILE cc_start: 0.7996 (mm) cc_final: 0.7723 (mm) REVERT: A 214 GLU cc_start: 0.6853 (mp0) cc_final: 0.6228 (mm-30) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.6712 time to fit residues: 41.7932 Evaluate side-chains 43 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 248 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 63 ASN A 68 HIS A 121 ASN A 212 GLN A 238 GLN A 346 GLN A 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.129558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.108318 restraints weight = 3058.996| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.07 r_work: 0.2836 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3161 Z= 0.167 Angle : 0.592 5.619 4304 Z= 0.315 Chirality : 0.042 0.139 480 Planarity : 0.004 0.034 543 Dihedral : 9.793 60.856 521 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.56 % Allowed : 13.14 % Favored : 84.29 % 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 are not related in a simple way. whole: 1.64 (0.44), residues: 372 helix: 1.28 (0.35), residues: 220 sheet: 1.45 (1.44), residues: 14 loop : 0.99 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.018 0.002 TYR A 361 PHE 0.014 0.002 PHE A 289 TRP 0.008 0.002 TRP A 175 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 3161) covalent geometry : angle 0.59193 / 0.31 ( 4304) hydrogen bonds : bond 0.05893 / 3.68 ( 167) hydrogen bonds : angle 4.61110 / 3.27 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.114 Fit side-chains REVERT: A 6 LYS cc_start: 0.8540 (mttt) cc_final: 0.8245 (mttt) REVERT: A 17 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 208 ARG cc_start: 0.7832 (ttt-90) cc_final: 0.7135 (ttp-170) REVERT: A 214 GLU cc_start: 0.7011 (mp0) cc_final: 0.6436 (tp30) outliers start: 8 outliers final: 1 residues processed: 51 average time/residue: 0.7429 time to fit residues: 38.6355 Evaluate side-chains 42 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.129956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.108732 restraints weight = 3090.702| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.01 r_work: 0.2832 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3161 Z= 0.149 Angle : 0.547 4.925 4304 Z= 0.287 Chirality : 0.040 0.132 480 Planarity : 0.004 0.034 543 Dihedral : 9.399 60.535 516 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.56 % Allowed : 13.46 % Favored : 83.97 % 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 are not related in a simple way. whole: 1.91 (0.44), residues: 372 helix: 1.60 (0.36), residues: 220 sheet: 1.87 (1.45), residues: 14 loop : 0.85 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.017 0.002 TYR A 361 PHE 0.013 0.002 PHE A 289 TRP 0.007 0.002 TRP A 175 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 3161) covalent geometry : angle 0.54690 / 0.29 ( 4304) hydrogen bonds : bond 0.05376 / 3.31 ( 167) hydrogen bonds : angle 4.36380 / 3.08 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.117 Fit side-chains REVERT: A 6 LYS cc_start: 0.8529 (mttt) cc_final: 0.8258 (mttt) REVERT: A 93 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7478 (mtm180) REVERT: A 208 ARG cc_start: 0.7888 (ttt-90) cc_final: 0.7184 (ttp-170) REVERT: A 214 GLU cc_start: 0.7018 (mp0) cc_final: 0.6451 (tp30) outliers start: 8 outliers final: 5 residues processed: 54 average time/residue: 0.7071 time to fit residues: 38.8931 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.134242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.118278 restraints weight = 3096.665| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 0.65 r_work: 0.2898 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3161 Z= 0.098 Angle : 0.456 4.622 4304 Z= 0.244 Chirality : 0.038 0.132 480 Planarity : 0.004 0.031 543 Dihedral : 9.119 60.486 516 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 4.17 % Allowed : 12.18 % Favored : 83.65 % 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 are not related in a simple way. whole: 2.32 (0.44), residues: 372 helix: 1.95 (0.36), residues: 220 sheet: 2.24 (1.53), residues: 14 loop : 0.95 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.013 0.001 TYR A 361 PHE 0.009 0.001 PHE A 163 TRP 0.005 0.001 TRP A 175 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 3161) covalent geometry : angle 0.45614 / 0.24 ( 4304) hydrogen bonds : bond 0.04060 / 2.51 ( 167) hydrogen bonds : angle 4.06840 / 2.86 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.065 Fit side-chains REVERT: A 93 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7500 (mtm180) REVERT: A 208 ARG cc_start: 0.7956 (ttt-90) cc_final: 0.7268 (ttp-170) REVERT: A 214 GLU cc_start: 0.7146 (mp0) cc_final: 0.6539 (tp30) REVERT: A 317 GLU cc_start: 0.7818 (pt0) cc_final: 0.7443 (mt-10) outliers start: 13 outliers final: 6 residues processed: 62 average time/residue: 0.6050 time to fit residues: 38.3392 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.0570 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.133113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.112738 restraints weight = 3093.386| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 0.98 r_work: 0.2870 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3161 Z= 0.108 Angle : 0.466 4.626 4304 Z= 0.247 Chirality : 0.038 0.132 480 Planarity : 0.003 0.030 543 Dihedral : 9.010 60.463 516 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.24 % Allowed : 14.42 % Favored : 83.33 % 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 are not related in a simple way. whole: 2.46 (0.44), residues: 372 helix: 2.06 (0.36), residues: 220 sheet: 2.49 (1.57), residues: 14 loop : 0.99 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.014 0.001 TYR A 361 PHE 0.010 0.001 PHE A 270 TRP 0.006 0.002 TRP A 281 HIS 0.001 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 3161) covalent geometry : angle 0.46614 / 0.25 ( 4304) hydrogen bonds : bond 0.04291 / 2.62 ( 167) hydrogen bonds : angle 4.00779 / 2.82 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.072 Fit side-chains REVERT: A 6 LYS cc_start: 0.8498 (mttt) cc_final: 0.8237 (mttp) REVERT: A 208 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7180 (ttp-170) REVERT: A 214 GLU cc_start: 0.7037 (mp0) cc_final: 0.6488 (tp30) REVERT: A 317 GLU cc_start: 0.7748 (pt0) cc_final: 0.7436 (mt-10) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.7025 time to fit residues: 37.9933 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.130750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.109926 restraints weight = 3099.239| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.98 r_work: 0.2773 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3161 Z= 0.136 Angle : 0.507 4.842 4304 Z= 0.266 Chirality : 0.039 0.132 480 Planarity : 0.004 0.029 543 Dihedral : 9.088 60.505 516 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.88 % Allowed : 14.10 % Favored : 83.01 % 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 are not related in a simple way. whole: 2.35 (0.43), residues: 372 helix: 1.98 (0.35), residues: 220 sheet: 2.57 (1.55), residues: 14 loop : 0.93 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.016 0.002 TYR A 361 PHE 0.011 0.002 PHE A 270 TRP 0.008 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 3161) covalent geometry : angle 0.50706 / 0.27 ( 4304) hydrogen bonds : bond 0.04905 / 2.98 ( 167) hydrogen bonds : angle 4.09648 / 2.89 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.111 Fit side-chains REVERT: A 6 LYS cc_start: 0.8488 (mttt) cc_final: 0.8234 (mttp) REVERT: A 41 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7606 (t0) REVERT: A 208 ARG cc_start: 0.7905 (ttt-90) cc_final: 0.7218 (ttp-170) REVERT: A 214 GLU cc_start: 0.7033 (mp0) cc_final: 0.6530 (tp30) REVERT: A 317 GLU cc_start: 0.7747 (pt0) cc_final: 0.7446 (mt-10) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.6378 time to fit residues: 39.7801 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.130719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.110089 restraints weight = 3132.540| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 0.97 r_work: 0.2779 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3161 Z= 0.130 Angle : 0.498 4.819 4304 Z= 0.263 Chirality : 0.039 0.132 480 Planarity : 0.004 0.030 543 Dihedral : 9.080 60.436 516 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.21 % Allowed : 14.10 % Favored : 82.69 % 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 are not related in a simple way. whole: 2.33 (0.43), residues: 372 helix: 1.96 (0.35), residues: 220 sheet: 2.60 (1.55), residues: 14 loop : 0.89 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.015 0.001 TYR A 361 PHE 0.011 0.002 PHE A 270 TRP 0.007 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 3161) covalent geometry : angle 0.49801 / 0.26 ( 4304) hydrogen bonds : bond 0.04778 / 2.91 ( 167) hydrogen bonds : angle 4.07977 / 2.88 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.125 Fit side-chains REVERT: A 6 LYS cc_start: 0.8490 (mttt) cc_final: 0.8230 (mttp) REVERT: A 41 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7579 (t0) REVERT: A 214 GLU cc_start: 0.7037 (mp0) cc_final: 0.6547 (tp30) REVERT: A 317 GLU cc_start: 0.7751 (pt0) cc_final: 0.7496 (mt-10) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.7474 time to fit residues: 42.6409 Evaluate side-chains 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.0010 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.133893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.113629 restraints weight = 3131.642| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.00 r_work: 0.2892 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3161 Z= 0.099 Angle : 0.448 4.623 4304 Z= 0.240 Chirality : 0.038 0.132 480 Planarity : 0.003 0.032 543 Dihedral : 8.946 60.370 516 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.53 % Allowed : 13.78 % Favored : 82.69 % 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 are not related in a simple way. whole: 2.50 (0.44), residues: 372 helix: 2.11 (0.35), residues: 220 sheet: 2.62 (1.58), residues: 14 loop : 0.95 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.012 0.001 TYR A 361 PHE 0.008 0.001 PHE A 163 TRP 0.005 0.001 TRP A 175 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 3161) covalent geometry : angle 0.44765 / 0.24 ( 4304) hydrogen bonds : bond 0.03998 / 2.45 ( 167) hydrogen bonds : angle 3.91307 / 2.75 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.148 Fit side-chains REVERT: A 6 LYS cc_start: 0.8485 (mttt) cc_final: 0.8238 (mttp) REVERT: A 41 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7624 (t0) REVERT: A 214 GLU cc_start: 0.6997 (mp0) cc_final: 0.6461 (tp30) REVERT: A 317 GLU cc_start: 0.7757 (pt0) cc_final: 0.7472 (mt-10) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.7857 time to fit residues: 45.6716 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.134834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117453 restraints weight = 3116.281| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 0.98 r_work: 0.2878 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3161 Z= 0.097 Angle : 0.446 4.553 4304 Z= 0.237 Chirality : 0.037 0.132 480 Planarity : 0.003 0.032 543 Dihedral : 8.799 60.281 516 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.88 % Allowed : 14.74 % Favored : 82.37 % 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 are not related in a simple way. whole: 2.64 (0.44), residues: 372 helix: 2.20 (0.36), residues: 220 sheet: 2.85 (1.60), residues: 14 loop : 1.04 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.013 0.001 TYR A 361 PHE 0.008 0.001 PHE A 163 TRP 0.005 0.001 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 3161) covalent geometry : angle 0.44589 / 0.24 ( 4304) hydrogen bonds : bond 0.03870 / 2.36 ( 167) hydrogen bonds : angle 3.84936 / 2.71 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.121 Fit side-chains REVERT: A 41 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7639 (t0) REVERT: A 214 GLU cc_start: 0.7057 (mp0) cc_final: 0.6635 (tp30) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.7592 time to fit residues: 41.8246 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.136522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.123248 restraints weight = 2995.092| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 0.53 r_work: 0.2974 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3161 Z= 0.090 Angle : 0.428 4.484 4304 Z= 0.228 Chirality : 0.037 0.131 480 Planarity : 0.003 0.032 543 Dihedral : 8.703 60.207 516 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.41 % 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 are not related in a simple way. whole: 2.77 (0.44), residues: 372 helix: 2.28 (0.36), residues: 220 sheet: 2.81 (1.60), residues: 14 loop : 1.17 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.012 0.001 TYR A 361 PHE 0.008 0.001 PHE A 163 TRP 0.003 0.001 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 ( 3161) covalent geometry : angle 0.42797 / 0.23 ( 4304) hydrogen bonds : bond 0.03603 / 2.20 ( 167) hydrogen bonds : angle 3.73252 / 2.62 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.078 Fit side-chains REVERT: A 41 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7698 (t0) REVERT: A 44 ASN cc_start: 0.6411 (m-40) cc_final: 0.5774 (t0) REVERT: A 93 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7673 (mtm180) REVERT: A 214 GLU cc_start: 0.7161 (mp0) cc_final: 0.6638 (tp30) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.7353 time to fit residues: 40.4358 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.0000 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.132235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.113909 restraints weight = 3069.430| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 0.98 r_work: 0.2823 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3161 Z= 0.123 Angle : 0.484 4.775 4304 Z= 0.255 Chirality : 0.038 0.131 480 Planarity : 0.003 0.031 543 Dihedral : 8.915 60.357 516 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.41 % 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 are not related in a simple way. whole: 2.63 (0.44), residues: 372 helix: 2.16 (0.35), residues: 220 sheet: 2.82 (1.57), residues: 14 loop : 1.10 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.016 0.001 TYR A 360 PHE 0.010 0.001 PHE A 270 TRP 0.008 0.002 TRP A 281 HIS 0.001 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3161) covalent geometry : angle 0.48380 / 0.25 ( 4304) hydrogen bonds : bond 0.04457 / 2.71 ( 167) hydrogen bonds : angle 3.88545 / 2.72 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.41 seconds wall clock time: 26 minutes 34.71 seconds (1594.71 seconds total)