Starting phenix.real_space_refine on Sat Apr 4 20:40:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbt_61325/04_2026/9jbt_61325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbt_61325/04_2026/9jbt_61325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jbt_61325/04_2026/9jbt_61325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbt_61325/04_2026/9jbt_61325.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbt_61325/04_2026/9jbt_61325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbt_61325/04_2026/9jbt_61325_neut.cif" } resolution = 3.2 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= -0.001 sd= 0.022 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 29 5.16 5 C 2066 2.51 5 N 491 2.21 5 O 515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3101 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3089 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 15, 'TRANS': 393} Chain breaks: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 0.85, per 1000 atoms: 0.27 Number of scatterers: 3101 At special positions: 0 Unit cell: (73.392, 50.04, 73.392, 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 29 16.00 O 515 8.00 N 491 7.00 C 2066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 81 " distance=2.03 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: 0.31 Conformation dependent library (CDL) restraints added in 95.3 milliseconds 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 90.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 8 through 10 No H-bonds generated for 'chain 'A' and resid 8 through 10' Processing helix chain 'A' and resid 11 through 27 removed outlier: 3.573A pdb=" N SER A 27 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 44 removed outlier: 4.066A pdb=" N LEU A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 102 Processing helix chain 'A' and resid 102 through 114 removed outlier: 4.217A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 139 removed outlier: 3.794A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 166 removed outlier: 3.802A pdb=" N ILE A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 4.113A pdb=" N MET A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.571A pdb=" N LEU A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 228 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.623A pdb=" N VAL A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 320 " --> pdb=" O MET A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 321 through 353 removed outlier: 4.941A pdb=" N ASN A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASN A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 371 Processing helix chain 'A' and resid 372 through 387 Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 417 through 444 Processing helix chain 'A' and resid 449 through 476 removed outlier: 3.650A pdb=" N HIS A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 480 through 497 Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 529 through 545 removed outlier: 3.806A pdb=" N CYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 75 261 hydrogen bonds defined for protein. 780 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: 0.44 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 921 1.34 - 1.46: 742 1.46 - 1.57: 1468 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 3176 Sorted by residual: bond pdb=" C PHE A 601 " pdb=" O PHE A 601 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C PHE A 601 " pdb=" OXT PHE A 601 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" CB PHE A 601 " pdb=" CG PHE A 601 " ideal model delta sigma weight residual 1.502 1.527 -0.025 2.30e-02 1.89e+03 1.14e+00 bond pdb=" CA THR A 18 " pdb=" C THR A 18 " ideal model delta sigma weight residual 1.524 1.516 0.007 1.32e-02 5.74e+03 3.08e-01 bond pdb=" CA ASP A 513 " pdb=" CB ASP A 513 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.58e-02 4.01e+03 2.90e-01 ... (remaining 3171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 4169 0.91 - 1.82: 129 1.82 - 2.73: 10 2.73 - 3.63: 6 3.63 - 4.54: 11 Bond angle restraints: 4325 Sorted by residual: angle pdb=" CA PHE A 601 " pdb=" CB PHE A 601 " pdb=" CG PHE A 601 " ideal model delta sigma weight residual 113.80 109.26 4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" N GLY A 32 " pdb=" CA GLY A 32 " pdb=" C GLY A 32 " ideal model delta sigma weight residual 114.16 110.27 3.89 2.00e+00 2.50e-01 3.78e+00 angle pdb=" CA GLN A 500 " pdb=" CB GLN A 500 " pdb=" CG GLN A 500 " ideal model delta sigma weight residual 114.10 117.98 -3.88 2.00e+00 2.50e-01 3.77e+00 angle pdb=" C VAL A 29 " pdb=" CA VAL A 29 " pdb=" CB VAL A 29 " ideal model delta sigma weight residual 111.79 108.43 3.36 1.91e+00 2.74e-01 3.10e+00 angle pdb=" C VAL A 192 " pdb=" CA VAL A 192 " pdb=" CB VAL A 192 " ideal model delta sigma weight residual 111.77 107.96 3.81 2.27e+00 1.94e-01 2.82e+00 ... (remaining 4320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.52: 1697 13.52 - 27.04: 93 27.04 - 40.57: 23 40.57 - 54.09: 8 54.09 - 67.61: 2 Dihedral angle restraints: 1823 sinusoidal: 653 harmonic: 1170 Sorted by residual: dihedral pdb=" CA LEU A 31 " pdb=" C LEU A 31 " pdb=" N GLY A 32 " pdb=" CA GLY A 32 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" N PHE A 529 " pdb=" CA PHE A 529 " pdb=" CB PHE A 529 " pdb=" CG PHE A 529 " ideal model delta sinusoidal sigma weight residual -180.00 -127.79 -52.21 3 1.50e+01 4.44e-03 9.09e+00 dihedral pdb=" N PHE A 227 " pdb=" CA PHE A 227 " pdb=" CB PHE A 227 " pdb=" CG PHE A 227 " ideal model delta sinusoidal sigma weight residual -60.00 -104.29 44.29 3 1.50e+01 4.44e-03 7.97e+00 ... (remaining 1820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 369 0.026 - 0.051: 87 0.051 - 0.077: 47 0.077 - 0.103: 17 0.103 - 0.129: 3 Chirality restraints: 523 Sorted by residual: chirality pdb=" CA ILE A 444 " pdb=" N ILE A 444 " pdb=" C ILE A 444 " pdb=" CB ILE A 444 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA PRO A 140 " pdb=" N PRO A 140 " pdb=" C PRO A 140 " pdb=" CB PRO A 140 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.75e-01 chirality pdb=" CA PRO A 169 " pdb=" N PRO A 169 " pdb=" C PRO A 169 " pdb=" CB PRO A 169 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 520 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 17 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C CYS A 17 " -0.027 2.00e-02 2.50e+03 pdb=" O CYS A 17 " 0.010 2.00e-02 2.50e+03 pdb=" N THR A 18 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 20 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C VAL A 20 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL A 20 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 21 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 15 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C MET A 15 " 0.024 2.00e-02 2.50e+03 pdb=" O MET A 15 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A 16 " -0.008 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 52 2.67 - 3.23: 3519 3.23 - 3.79: 5064 3.79 - 4.34: 7195 4.34 - 4.90: 11473 Nonbonded interactions: 27303 Sorted by model distance: nonbonded pdb=" O LEU A 522 " pdb=" OG SER A 525 " model vdw 2.114 3.040 nonbonded pdb=" O LYS A 350 " pdb=" N GLY A 355 " model vdw 2.159 3.120 nonbonded pdb=" OE1 GLN A 371 " pdb=" NH1 ARG A 461 " model vdw 2.282 3.120 nonbonded pdb=" O TYR A 187 " pdb=" OG SER A 190 " model vdw 2.337 3.040 nonbonded pdb=" O THR A 164 " pdb=" OG1 THR A 167 " model vdw 2.351 3.040 ... (remaining 27298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.150 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.002 0.028 3177 Z= 0.117 Angle : 0.431 4.543 4327 Z= 0.244 Chirality : 0.032 0.129 523 Planarity : 0.004 0.033 520 Dihedral : 10.228 67.608 1068 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.53 % Allowed : 3.36 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.68 (0.44), residues: 401 helix: 1.99 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 1.15 (0.81), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 540 TYR 0.005 0.001 TYR A 48 PHE 0.008 0.001 PHE A 172 TRP 0.003 0.001 TRP A 74 HIS 0.001 0.000 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3176) covalent geometry : angle 0.43059 ( 4325) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.34678 ( 2) hydrogen bonds : bond 0.27146 ( 261) hydrogen bonds : angle 7.86453 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 425 MET cc_start: 0.6736 (tmt) cc_final: 0.6459 (tmm) outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 0.0369 time to fit residues: 6.1969 Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 529 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.193907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180171 restraints weight = 4543.560| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.40 r_work: 0.4036 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3177 Z= 0.167 Angle : 0.620 7.488 4327 Z= 0.321 Chirality : 0.042 0.160 523 Planarity : 0.005 0.054 520 Dihedral : 5.769 59.482 435 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.67 % Allowed : 12.54 % Favored : 83.79 % 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: 2.49 (0.42), residues: 401 helix: 1.77 (0.27), residues: 345 sheet: None (None), residues: 0 loop : 1.20 (1.02), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.021 0.002 TYR A 472 PHE 0.020 0.002 PHE A 438 TRP 0.007 0.001 TRP A 14 HIS 0.001 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3176) covalent geometry : angle 0.61972 ( 4325) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.25140 ( 2) hydrogen bonds : bond 0.04964 ( 261) hydrogen bonds : angle 5.18144 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.106 Fit side-chains REVERT: A 201 TYR cc_start: 0.6580 (t80) cc_final: 0.6323 (t80) REVERT: A 214 TRP cc_start: 0.7996 (t60) cc_final: 0.7647 (t60) REVERT: A 425 MET cc_start: 0.6581 (tmt) cc_final: 0.6273 (tmm) REVERT: A 480 GLN cc_start: 0.8221 (mp10) cc_final: 0.7762 (mp10) outliers start: 12 outliers final: 6 residues processed: 110 average time/residue: 0.0372 time to fit residues: 5.6149 Evaluate side-chains 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 529 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 84 GLN A 432 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.198994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184810 restraints weight = 4503.092| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.48 r_work: 0.4053 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3177 Z= 0.160 Angle : 0.619 7.681 4327 Z= 0.313 Chirality : 0.041 0.193 523 Planarity : 0.004 0.060 520 Dihedral : 5.289 55.587 432 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.45 % Allowed : 18.04 % Favored : 79.51 % 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: 2.22 (0.42), residues: 401 helix: 1.52 (0.27), residues: 349 sheet: None (None), residues: 0 loop : 1.62 (1.05), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 539 TYR 0.015 0.002 TYR A 187 PHE 0.014 0.002 PHE A 438 TRP 0.004 0.001 TRP A 229 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3176) covalent geometry : angle 0.61746 ( 4325) SS BOND : bond 0.00844 ( 1) SS BOND : angle 2.02280 ( 2) hydrogen bonds : bond 0.04408 ( 261) hydrogen bonds : angle 4.98358 ( 780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.106 Fit side-chains REVERT: A 425 MET cc_start: 0.6560 (tmt) cc_final: 0.5918 (tmm) REVERT: A 480 GLN cc_start: 0.8073 (mp10) cc_final: 0.7699 (mp10) REVERT: A 511 GLN cc_start: 0.8893 (mp10) cc_final: 0.8422 (mp10) outliers start: 8 outliers final: 2 residues processed: 97 average time/residue: 0.0358 time to fit residues: 4.7951 Evaluate side-chains 92 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 502 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.196684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182810 restraints weight = 4597.794| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.43 r_work: 0.4058 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3177 Z= 0.166 Angle : 0.611 7.133 4327 Z= 0.308 Chirality : 0.042 0.208 523 Planarity : 0.004 0.059 520 Dihedral : 4.365 19.011 430 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.98 % Allowed : 18.35 % Favored : 77.68 % 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: 2.00 (0.42), residues: 401 helix: 1.38 (0.27), residues: 349 sheet: None (None), residues: 0 loop : 1.48 (1.05), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.015 0.002 TYR A 187 PHE 0.019 0.002 PHE A 438 TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3176) covalent geometry : angle 0.60879 ( 4325) SS BOND : bond 0.00466 ( 1) SS BOND : angle 2.23660 ( 2) hydrogen bonds : bond 0.04213 ( 261) hydrogen bonds : angle 4.97409 ( 780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 425 MET cc_start: 0.6597 (tmt) cc_final: 0.5939 (tmm) REVERT: A 480 GLN cc_start: 0.7906 (mp10) cc_final: 0.7655 (mp10) outliers start: 13 outliers final: 5 residues processed: 101 average time/residue: 0.0347 time to fit residues: 4.9049 Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 502 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.0040 chunk 25 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.203514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.189677 restraints weight = 4442.042| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.41 r_work: 0.4094 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3177 Z= 0.149 Angle : 0.597 7.606 4327 Z= 0.302 Chirality : 0.042 0.206 523 Planarity : 0.004 0.056 520 Dihedral : 4.287 18.096 430 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.14 % Allowed : 21.71 % Favored : 76.15 % 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: 2.04 (0.42), residues: 401 helix: 1.44 (0.27), residues: 349 sheet: None (None), residues: 0 loop : 1.32 (1.06), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.014 0.002 TYR A 187 PHE 0.014 0.002 PHE A 438 TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3176) covalent geometry : angle 0.59639 ( 4325) SS BOND : bond 0.00371 ( 1) SS BOND : angle 1.66284 ( 2) hydrogen bonds : bond 0.03932 ( 261) hydrogen bonds : angle 4.89560 ( 780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.118 Fit side-chains REVERT: A 183 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5279 (mmp) REVERT: A 201 TYR cc_start: 0.6218 (t80) cc_final: 0.5888 (t80) REVERT: A 425 MET cc_start: 0.6550 (tmt) cc_final: 0.5972 (tmm) REVERT: A 511 GLN cc_start: 0.8875 (mp10) cc_final: 0.8436 (mp10) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.0349 time to fit residues: 4.5760 Evaluate side-chains 97 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 502 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.198367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.184794 restraints weight = 4518.335| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.41 r_work: 0.4057 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3177 Z= 0.185 Angle : 0.633 7.661 4327 Z= 0.321 Chirality : 0.043 0.206 523 Planarity : 0.004 0.056 520 Dihedral : 4.445 18.855 430 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.98 % Allowed : 21.71 % Favored : 74.31 % 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: 1.76 (0.42), residues: 401 helix: 1.26 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.17 (1.08), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.012 0.002 TYR A 187 PHE 0.012 0.002 PHE A 503 TRP 0.008 0.001 TRP A 74 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 3176) covalent geometry : angle 0.63266 ( 4325) SS BOND : bond 0.00389 ( 1) SS BOND : angle 1.55681 ( 2) hydrogen bonds : bond 0.04254 ( 261) hydrogen bonds : angle 5.05219 ( 780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.100 Fit side-chains REVERT: A 183 MET cc_start: 0.5866 (OUTLIER) cc_final: 0.5345 (mmp) REVERT: A 317 HIS cc_start: 0.5981 (t70) cc_final: 0.5080 (m90) REVERT: A 425 MET cc_start: 0.6603 (tmt) cc_final: 0.6003 (tmm) outliers start: 13 outliers final: 6 residues processed: 99 average time/residue: 0.0324 time to fit residues: 4.4855 Evaluate side-chains 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.200846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.187384 restraints weight = 4509.422| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.39 r_work: 0.4073 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3177 Z= 0.162 Angle : 0.637 7.763 4327 Z= 0.321 Chirality : 0.042 0.203 523 Planarity : 0.004 0.054 520 Dihedral : 4.382 19.020 430 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 24.16 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.87 (0.42), residues: 401 helix: 1.36 (0.27), residues: 343 sheet: None (None), residues: 0 loop : 1.02 (1.05), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.012 0.002 TYR A 187 PHE 0.014 0.002 PHE A 503 TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3176) covalent geometry : angle 0.63683 ( 4325) SS BOND : bond 0.00293 ( 1) SS BOND : angle 1.25783 ( 2) hydrogen bonds : bond 0.04050 ( 261) hydrogen bonds : angle 5.01379 ( 780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.113 Fit side-chains REVERT: A 183 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.5305 (mmp) REVERT: A 214 TRP cc_start: 0.7903 (t60) cc_final: 0.7528 (t60) REVERT: A 317 HIS cc_start: 0.5911 (t70) cc_final: 0.4997 (m90) REVERT: A 425 MET cc_start: 0.6518 (tmt) cc_final: 0.5991 (tmm) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.0345 time to fit residues: 4.7018 Evaluate side-chains 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 502 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.194894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.181409 restraints weight = 4672.610| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.45 r_work: 0.4060 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3177 Z= 0.179 Angle : 0.650 8.531 4327 Z= 0.326 Chirality : 0.043 0.199 523 Planarity : 0.004 0.055 520 Dihedral : 4.450 20.248 430 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.75 % Allowed : 22.63 % Favored : 74.62 % 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: 1.66 (0.42), residues: 401 helix: 1.19 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.09 (1.09), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 337 TYR 0.011 0.002 TYR A 187 PHE 0.044 0.002 PHE A 503 TRP 0.005 0.001 TRP A 74 HIS 0.001 0.000 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3176) covalent geometry : angle 0.64963 ( 4325) SS BOND : bond 0.00259 ( 1) SS BOND : angle 1.27075 ( 2) hydrogen bonds : bond 0.04171 ( 261) hydrogen bonds : angle 5.10891 ( 780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.133 Fit side-chains REVERT: A 183 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5399 (mmp) REVERT: A 317 HIS cc_start: 0.5959 (t70) cc_final: 0.5047 (m90) REVERT: A 425 MET cc_start: 0.6499 (tmt) cc_final: 0.5983 (tmm) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.0309 time to fit residues: 4.2002 Evaluate side-chains 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.200490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.186598 restraints weight = 4617.004| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.45 r_work: 0.4074 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3177 Z= 0.167 Angle : 0.652 8.769 4327 Z= 0.325 Chirality : 0.043 0.197 523 Planarity : 0.004 0.054 520 Dihedral : 4.458 20.787 430 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.75 % Allowed : 22.94 % Favored : 74.31 % 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: 1.62 (0.42), residues: 401 helix: 1.17 (0.27), residues: 348 sheet: None (None), residues: 0 loop : 1.01 (1.09), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.011 0.002 TYR A 187 PHE 0.041 0.002 PHE A 503 TRP 0.004 0.001 TRP A 229 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3176) covalent geometry : angle 0.65218 ( 4325) SS BOND : bond 0.00228 ( 1) SS BOND : angle 1.13189 ( 2) hydrogen bonds : bond 0.04093 ( 261) hydrogen bonds : angle 5.14659 ( 780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.112 Fit side-chains REVERT: A 183 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5449 (mmp) REVERT: A 317 HIS cc_start: 0.5949 (t70) cc_final: 0.5030 (m90) REVERT: A 425 MET cc_start: 0.6536 (tmt) cc_final: 0.6022 (tmm) REVERT: A 511 GLN cc_start: 0.8722 (mp10) cc_final: 0.8357 (mp10) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.0353 time to fit residues: 4.6489 Evaluate side-chains 97 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.200217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.186627 restraints weight = 4525.635| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.39 r_work: 0.4081 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3177 Z= 0.173 Angle : 0.665 8.850 4327 Z= 0.330 Chirality : 0.043 0.195 523 Planarity : 0.004 0.054 520 Dihedral : 4.509 21.324 430 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.45 % Allowed : 23.85 % Favored : 73.70 % 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: 1.55 (0.42), residues: 401 helix: 1.15 (0.27), residues: 347 sheet: None (None), residues: 0 loop : 0.80 (1.07), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.010 0.002 TYR A 341 PHE 0.046 0.002 PHE A 503 TRP 0.004 0.001 TRP A 74 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3176) covalent geometry : angle 0.66460 ( 4325) SS BOND : bond 0.00215 ( 1) SS BOND : angle 1.12785 ( 2) hydrogen bonds : bond 0.04136 ( 261) hydrogen bonds : angle 5.19008 ( 780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.109 Fit side-chains REVERT: A 183 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5462 (mmp) REVERT: A 317 HIS cc_start: 0.5976 (t70) cc_final: 0.5064 (m90) REVERT: A 425 MET cc_start: 0.6521 (tmt) cc_final: 0.6010 (tmm) REVERT: A 511 GLN cc_start: 0.8741 (mp10) cc_final: 0.8364 (mp10) outliers start: 8 outliers final: 5 residues processed: 95 average time/residue: 0.0337 time to fit residues: 4.4324 Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.199148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.185491 restraints weight = 4652.384| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.48 r_work: 0.4100 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3177 Z= 0.154 Angle : 0.648 9.036 4327 Z= 0.321 Chirality : 0.042 0.197 523 Planarity : 0.004 0.054 520 Dihedral : 4.433 21.039 430 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 23.85 % Favored : 74.01 % 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: 1.78 (0.42), residues: 401 helix: 1.33 (0.27), residues: 343 sheet: None (None), residues: 0 loop : 0.76 (1.05), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 539 TYR 0.010 0.002 TYR A 187 PHE 0.052 0.002 PHE A 503 TRP 0.005 0.001 TRP A 387 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3176) covalent geometry : angle 0.64800 ( 4325) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.96783 ( 2) hydrogen bonds : bond 0.03927 ( 261) hydrogen bonds : angle 5.10722 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 826.68 seconds wall clock time: 14 minutes 51.53 seconds (891.53 seconds total)