Starting phenix.real_space_refine on Fri Aug 22 13:25:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvf_34125/08_2025/7yvf_34125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvf_34125/08_2025/7yvf_34125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvf_34125/08_2025/7yvf_34125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvf_34125/08_2025/7yvf_34125.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvf_34125/08_2025/7yvf_34125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvf_34125/08_2025/7yvf_34125.cif" } resolution = 3.4 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= 0.030 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 14 5.16 5 C 2094 2.51 5 N 562 2.21 5 O 613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "B" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1511 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 0.97, per 1000 atoms: 0.30 Number of scatterers: 3283 At special positions: 0 Unit cell: (74.62, 90.2, 84.46, 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 14 16.00 O 613 8.00 N 562 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 157.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 7 sheets defined 13.4% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.943A pdb=" N ASP A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 84 " --> pdb=" O SER A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.593A pdb=" N THR C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.913A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.616A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.227A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.529A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.932A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.565A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.629A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.566A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.650A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 100 hydrogen bonds defined for protein. 228 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: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1053 1.34 - 1.46: 902 1.46 - 1.58: 1403 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3374 Sorted by residual: bond pdb=" C HIS B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.340 1.262 0.078 5.87e-02 2.90e+02 1.77e+00 bond pdb=" C HIS C 104 " pdb=" N ASN C 105 " ideal model delta sigma weight residual 1.331 1.303 0.028 2.22e-02 2.03e+03 1.55e+00 bond pdb=" CD2 TYR B 495 " pdb=" CE2 TYR B 495 " ideal model delta sigma weight residual 1.382 1.345 0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CG1 ILE B 472 " pdb=" CD1 ILE B 472 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.31e+00 bond pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 ... (remaining 3369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 4323 1.42 - 2.83: 225 2.83 - 4.25: 40 4.25 - 5.67: 9 5.67 - 7.08: 3 Bond angle restraints: 4600 Sorted by residual: angle pdb=" CA CYS B 488 " pdb=" CB CYS B 488 " pdb=" SG CYS B 488 " ideal model delta sigma weight residual 114.40 121.25 -6.85 2.30e+00 1.89e-01 8.87e+00 angle pdb=" C SER A 51 " pdb=" N ASN A 52 " pdb=" CA ASN A 52 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.68e+00 angle pdb=" N PRO B 521 " pdb=" CA PRO B 521 " pdb=" C PRO B 521 " ideal model delta sigma weight residual 112.92 105.84 7.08 2.73e+00 1.34e-01 6.73e+00 angle pdb=" N ASN B 477 " pdb=" CA ASN B 477 " pdb=" C ASN B 477 " ideal model delta sigma weight residual 110.14 106.19 3.95 1.55e+00 4.16e-01 6.49e+00 angle pdb=" C ASN B 487 " pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.21e+00 ... (remaining 4595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.83: 1648 11.83 - 23.66: 224 23.66 - 35.48: 76 35.48 - 47.31: 17 47.31 - 59.14: 8 Dihedral angle restraints: 1973 sinusoidal: 750 harmonic: 1223 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 89 " pdb=" CB CYS A 89 " ideal model delta sinusoidal sigma weight residual 93.00 149.96 -56.96 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.96 53.04 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 303 0.038 - 0.077: 139 0.077 - 0.115: 44 0.115 - 0.154: 12 0.154 - 0.192: 2 Chirality restraints: 500 Sorted by residual: chirality pdb=" CB THR C 106 " pdb=" CA THR C 106 " pdb=" OG1 THR C 106 " pdb=" CG2 THR C 106 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA THR C 15 " pdb=" N THR C 15 " pdb=" C THR C 15 " pdb=" CB THR C 15 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 497 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.012 2.00e-02 2.50e+03 2.07e-02 8.55e+00 pdb=" CG TYR B 495 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 35 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C TYR A 35 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR A 35 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP A 36 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 53 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ILE C 53 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE C 53 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 54 " 0.015 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 514 2.75 - 3.29: 2931 3.29 - 3.83: 4949 3.83 - 4.36: 6045 4.36 - 4.90: 10813 Nonbonded interactions: 25252 Sorted by model distance: nonbonded pdb=" O VAL B 367 " pdb=" ND2 ASN B 370 " model vdw 2.217 3.120 nonbonded pdb=" O GLY C 33 " pdb=" NH1 ARG C 100 " model vdw 2.253 3.120 nonbonded pdb=" NH1 ARG B 457 " pdb=" O SER B 459 " model vdw 2.257 3.120 nonbonded pdb=" O TRP B 353 " pdb=" NH1 ARG B 466 " model vdw 2.306 3.120 nonbonded pdb=" O ARG C 66 " pdb=" OG SER C 67 " model vdw 2.334 3.040 ... (remaining 25247 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: 8.550 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.970 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.006 0.078 3380 Z= 0.256 Angle : 0.760 7.082 4612 Z= 0.421 Chirality : 0.049 0.192 500 Planarity : 0.006 0.043 594 Dihedral : 12.395 59.137 1177 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.64 % Favored : 91.89 % Rotamer: Outliers : 0.56 % Allowed : 5.08 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.35), residues: 419 helix: -4.76 (0.45), residues: 28 sheet: -1.73 (0.40), residues: 158 loop : -3.05 (0.33), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 100 TYR 0.050 0.002 TYR B 495 PHE 0.017 0.001 PHE B 392 TRP 0.014 0.001 TRP C 55 HIS 0.006 0.002 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 3374) covalent geometry : angle 0.75531 ( 4600) SS BOND : bond 0.00661 ( 6) SS BOND : angle 1.74028 ( 12) hydrogen bonds : bond 0.18110 ( 100) hydrogen bonds : angle 7.37075 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.126 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 0.0973 time to fit residues: 9.7584 Evaluate side-chains 62 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 54 GLN C 78 ASN C 86 ASN B 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.087463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075702 restraints weight = 7563.737| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.58 r_work: 0.2936 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3380 Z= 0.137 Angle : 0.631 7.778 4612 Z= 0.325 Chirality : 0.046 0.149 500 Planarity : 0.005 0.037 594 Dihedral : 5.561 33.129 468 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.77 % Favored : 94.99 % Rotamer: Outliers : 2.26 % Allowed : 17.23 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.37), residues: 419 helix: -5.04 (0.20), residues: 28 sheet: -1.09 (0.40), residues: 153 loop : -2.38 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 452 TYR 0.005 0.001 TYR B 351 PHE 0.014 0.001 PHE B 375 TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3374) covalent geometry : angle 0.62709 ( 4600) SS BOND : bond 0.00663 ( 6) SS BOND : angle 1.53979 ( 12) hydrogen bonds : bond 0.03583 ( 100) hydrogen bonds : angle 5.83947 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.129 Fit side-chains REVERT: B 418 ILE cc_start: 0.9341 (pt) cc_final: 0.8999 (mt) REVERT: B 420 ASP cc_start: 0.8508 (t0) cc_final: 0.7896 (t0) outliers start: 8 outliers final: 3 residues processed: 77 average time/residue: 0.0855 time to fit residues: 7.7811 Evaluate side-chains 68 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.087158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075468 restraints weight = 7534.070| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.56 r_work: 0.2935 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3380 Z= 0.137 Angle : 0.625 8.192 4612 Z= 0.317 Chirality : 0.045 0.147 500 Planarity : 0.005 0.033 594 Dihedral : 5.020 33.254 466 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.82 % Allowed : 18.93 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.37), residues: 419 helix: -5.02 (0.22), residues: 28 sheet: -0.69 (0.40), residues: 155 loop : -2.08 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 452 TYR 0.009 0.001 TYR B 489 PHE 0.011 0.001 PHE B 375 TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3374) covalent geometry : angle 0.62025 ( 4600) SS BOND : bond 0.00674 ( 6) SS BOND : angle 1.68470 ( 12) hydrogen bonds : bond 0.03260 ( 100) hydrogen bonds : angle 5.35556 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.172 Fit side-chains REVERT: A 26 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6767 (mtt180) REVERT: B 418 ILE cc_start: 0.9307 (pt) cc_final: 0.9069 (mt) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.0648 time to fit residues: 5.6516 Evaluate side-chains 67 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain B residue 440 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.085213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073642 restraints weight = 7571.200| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.58 r_work: 0.2909 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3380 Z= 0.183 Angle : 0.659 9.831 4612 Z= 0.334 Chirality : 0.046 0.162 500 Planarity : 0.005 0.034 594 Dihedral : 5.223 33.583 466 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.52 % Allowed : 18.64 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.38), residues: 419 helix: -4.87 (0.36), residues: 28 sheet: -0.47 (0.40), residues: 157 loop : -1.92 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 452 TYR 0.007 0.001 TYR C 96 PHE 0.010 0.001 PHE B 375 TRP 0.008 0.001 TRP A 99 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3374) covalent geometry : angle 0.65169 ( 4600) SS BOND : bond 0.00697 ( 6) SS BOND : angle 2.00753 ( 12) hydrogen bonds : bond 0.03456 ( 100) hydrogen bonds : angle 5.27682 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.099 Fit side-chains REVERT: B 418 ILE cc_start: 0.9354 (pt) cc_final: 0.9103 (mt) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.0766 time to fit residues: 6.8598 Evaluate side-chains 71 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 0.0170 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076857 restraints weight = 7517.534| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.60 r_work: 0.2966 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3380 Z= 0.104 Angle : 0.613 10.771 4612 Z= 0.301 Chirality : 0.044 0.147 500 Planarity : 0.004 0.029 594 Dihedral : 4.781 33.340 466 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.67 % Allowed : 18.93 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.38), residues: 419 helix: -4.90 (0.34), residues: 28 sheet: -0.08 (0.42), residues: 147 loop : -1.78 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 452 TYR 0.007 0.001 TYR B 489 PHE 0.010 0.001 PHE B 400 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3374) covalent geometry : angle 0.60791 ( 4600) SS BOND : bond 0.00571 ( 6) SS BOND : angle 1.62044 ( 12) hydrogen bonds : bond 0.02742 ( 100) hydrogen bonds : angle 5.08025 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.125 Fit side-chains REVERT: B 365 TYR cc_start: 0.8833 (m-80) cc_final: 0.8601 (m-80) outliers start: 13 outliers final: 8 residues processed: 78 average time/residue: 0.0562 time to fit residues: 5.4151 Evaluate side-chains 70 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.076349 restraints weight = 7513.915| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.58 r_work: 0.2959 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3380 Z= 0.135 Angle : 0.634 10.025 4612 Z= 0.314 Chirality : 0.045 0.147 500 Planarity : 0.004 0.029 594 Dihedral : 4.821 32.553 466 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.52 % Allowed : 20.06 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.39), residues: 419 helix: -4.80 (0.43), residues: 28 sheet: -0.20 (0.41), residues: 157 loop : -1.64 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 452 TYR 0.007 0.001 TYR C 96 PHE 0.009 0.001 PHE B 400 TRP 0.006 0.001 TRP A 99 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3374) covalent geometry : angle 0.62741 ( 4600) SS BOND : bond 0.00600 ( 6) SS BOND : angle 1.87211 ( 12) hydrogen bonds : bond 0.02939 ( 100) hydrogen bonds : angle 5.07204 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.109 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.0654 time to fit residues: 6.4305 Evaluate side-chains 76 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.076211 restraints weight = 7613.014| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.57 r_work: 0.2956 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3380 Z= 0.143 Angle : 0.652 10.933 4612 Z= 0.321 Chirality : 0.045 0.148 500 Planarity : 0.004 0.029 594 Dihedral : 4.889 32.057 466 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.80 % Allowed : 20.90 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.39), residues: 419 helix: -4.75 (0.49), residues: 28 sheet: -0.10 (0.41), residues: 152 loop : -1.62 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.007 0.001 TYR C 96 PHE 0.009 0.001 PHE B 400 TRP 0.006 0.001 TRP A 99 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3374) covalent geometry : angle 0.64396 ( 4600) SS BOND : bond 0.00621 ( 6) SS BOND : angle 2.07046 ( 12) hydrogen bonds : bond 0.02983 ( 100) hydrogen bonds : angle 5.13059 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.127 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 80 average time/residue: 0.0720 time to fit residues: 7.0241 Evaluate side-chains 77 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 0.0020 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.088071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.076474 restraints weight = 7708.719| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.60 r_work: 0.2961 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3380 Z= 0.129 Angle : 0.659 11.879 4612 Z= 0.321 Chirality : 0.045 0.171 500 Planarity : 0.004 0.029 594 Dihedral : 4.859 32.686 466 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.52 % Allowed : 20.62 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.39), residues: 419 helix: -4.77 (0.46), residues: 28 sheet: -0.02 (0.42), residues: 152 loop : -1.53 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.007 0.001 TYR C 96 PHE 0.010 0.001 PHE B 400 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3374) covalent geometry : angle 0.65291 ( 4600) SS BOND : bond 0.00586 ( 6) SS BOND : angle 1.81669 ( 12) hydrogen bonds : bond 0.02872 ( 100) hydrogen bonds : angle 5.12254 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.122 Fit side-chains REVERT: B 365 TYR cc_start: 0.8900 (m-80) cc_final: 0.8634 (m-80) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.0630 time to fit residues: 5.9996 Evaluate side-chains 76 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076509 restraints weight = 7641.964| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.59 r_work: 0.2959 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3380 Z= 0.134 Angle : 0.655 12.203 4612 Z= 0.319 Chirality : 0.045 0.160 500 Planarity : 0.004 0.029 594 Dihedral : 4.855 32.162 466 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.52 % Allowed : 21.19 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.39), residues: 419 helix: -4.75 (0.48), residues: 28 sheet: -0.01 (0.42), residues: 152 loop : -1.52 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 66 TYR 0.007 0.001 TYR C 96 PHE 0.010 0.001 PHE B 400 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3374) covalent geometry : angle 0.64908 ( 4600) SS BOND : bond 0.00553 ( 6) SS BOND : angle 1.83733 ( 12) hydrogen bonds : bond 0.02906 ( 100) hydrogen bonds : angle 5.15807 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.091 Fit side-chains REVERT: B 365 TYR cc_start: 0.8981 (m-80) cc_final: 0.8679 (m-80) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.0626 time to fit residues: 6.0030 Evaluate side-chains 78 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.086948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075555 restraints weight = 7584.611| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.54 r_work: 0.2937 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3380 Z= 0.170 Angle : 0.691 11.901 4612 Z= 0.340 Chirality : 0.046 0.155 500 Planarity : 0.004 0.030 594 Dihedral : 5.124 31.853 466 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.24 % Allowed : 21.75 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.40), residues: 419 helix: -4.74 (0.49), residues: 28 sheet: -0.12 (0.41), residues: 159 loop : -1.48 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 66 TYR 0.012 0.001 TYR B 489 PHE 0.009 0.001 PHE B 400 TRP 0.008 0.001 TRP A 99 HIS 0.002 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3374) covalent geometry : angle 0.68490 ( 4600) SS BOND : bond 0.00543 ( 6) SS BOND : angle 1.93083 ( 12) hydrogen bonds : bond 0.03223 ( 100) hydrogen bonds : angle 5.18071 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.142 Fit side-chains REVERT: B 365 TYR cc_start: 0.9067 (m-80) cc_final: 0.8840 (m-80) outliers start: 15 outliers final: 14 residues processed: 76 average time/residue: 0.0575 time to fit residues: 5.4501 Evaluate side-chains 76 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.077376 restraints weight = 7640.986| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.59 r_work: 0.2973 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 3380 Z= 0.135 Angle : 0.708 13.209 4612 Z= 0.343 Chirality : 0.046 0.279 500 Planarity : 0.004 0.028 594 Dihedral : 4.890 30.739 466 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.95 % Allowed : 21.75 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.39), residues: 419 helix: -4.72 (0.52), residues: 27 sheet: 0.13 (0.42), residues: 149 loop : -1.52 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.006 0.001 TYR B 351 PHE 0.010 0.001 PHE B 400 TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3374) covalent geometry : angle 0.68835 ( 4600) SS BOND : bond 0.01001 ( 6) SS BOND : angle 3.35534 ( 12) hydrogen bonds : bond 0.02859 ( 100) hydrogen bonds : angle 5.09990 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1127.05 seconds wall clock time: 19 minutes 55.60 seconds (1195.60 seconds total)