Starting phenix.real_space_refine on Fri Sep 11 02:42:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrz_14923/09_2026/7zrz_14923.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 18 5.16 5 C 3915 2.51 5 N 1148 2.21 5 O 1423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6580 Number of models: 1 Model: "" Number of chains: 5 Chain: "AP1" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1435 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 169} Chain breaks: 1 Chain: "BP4" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 861 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "CP1" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1791 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "DP1" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 848 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "ZN1" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNAv2': 77} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 17, 'rna3p': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.28, per 1000 atoms: 0.19 Number of scatterers: 6580 At special positions: 0 Unit cell: (86.58, 71.76, 120.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 76 15.00 O 1423 8.00 N 1148 7.00 C 3915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 270.7 milliseconds 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 7 sheets defined 30.6% alpha, 19.1% beta 27 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'AP1' and resid 15 through 26 removed outlier: 3.729A pdb=" N VALAP1 19 " --> pdb=" O GLYAP1 15 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLNAP1 20 " --> pdb=" O ALAAP1 16 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 53 through 63 Processing helix chain 'AP1' and resid 214 through 231 removed outlier: 3.709A pdb=" N ARGAP1 230 " --> pdb=" O ASPAP1 226 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLYAP1 231 " --> pdb=" O LEUAP1 227 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 271 through 285 removed outlier: 3.554A pdb=" N VALAP1 275 " --> pdb=" O LEUAP1 271 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALAAP1 276 " --> pdb=" O GLNAP1 272 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALAAP1 277 " --> pdb=" O ASPAP1 273 " (cutoff:3.500A) Processing helix chain 'BP4' and resid 338 through 352 removed outlier: 4.361A pdb=" N LYSBP4 352 " --> pdb=" O TYRBP4 348 " (cutoff:3.500A) Processing helix chain 'BP4' and resid 400 through 411 Processing helix chain 'CP1' and resid 50 through 61 removed outlier: 3.792A pdb=" N ARGCP1 54 " --> pdb=" O ALACP1 50 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEUCP1 55 " --> pdb=" O GLNCP1 51 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARGCP1 56 " --> pdb=" O ALACP1 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUCP1 61 " --> pdb=" O ARGCP1 57 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 62 through 67 removed outlier: 3.675A pdb=" N ALACP1 67 " --> pdb=" O TRPCP1 63 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 73 through 77 removed outlier: 3.520A pdb=" N SERCP1 76 " --> pdb=" O ARGCP1 73 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEUCP1 77 " --> pdb=" O LEUCP1 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'CP1' and resid 73 through 77' Processing helix chain 'CP1' and resid 96 through 101 Processing helix chain 'CP1' and resid 113 through 124 Processing helix chain 'CP1' and resid 151 through 163 removed outlier: 3.635A pdb=" N TYRCP1 155 " --> pdb=" O THRCP1 151 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 454 through 458 removed outlier: 3.848A pdb=" N VALCP1 458 " --> pdb=" O ALACP1 455 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 484 through 496 Processing helix chain 'DP1' and resid 57 through 73 Processing helix chain 'DP1' and resid 115 through 131 removed outlier: 3.800A pdb=" N ILEDP1 119 " --> pdb=" O SERDP1 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AP1' and resid 31 through 32 removed outlier: 3.571A pdb=" N ARGAP1 31 " --> pdb=" O LEUAP1 51 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SERAP1 11 " --> pdb=" O LEUAP1 52 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEUAP1 2 " --> pdb=" O THRAP1 67 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VALAP1 69 " --> pdb=" O LEUAP1 2 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VALAP1 4 " --> pdb=" O VALAP1 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AP1' and resid 233 through 236 removed outlier: 3.670A pdb=" N PHEAP1 233 " --> pdb=" O TYRAP1 247 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUAP1 288 " --> pdb=" O LEUAP1 304 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SERAP1 292 " --> pdb=" O VALAP1 300 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VALAP1 300 " --> pdb=" O SERAP1 292 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VALDP1 144 " --> pdb=" O THRDP1 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AP1' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'BP4' and resid 354 through 358 removed outlier: 3.598A pdb=" N VALBP4 355 " --> pdb=" O TYRBP4 369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEUBP4 366 " --> pdb=" O VALBP4 382 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEUBP4 418 " --> pdb=" O LEUBP4 450 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHECP1 515 " --> pdb=" O LEUCP1 500 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEUCP1 500 " --> pdb=" O PHECP1 515 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHECP1 450 " --> pdb=" O METCP1 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'CP1' and resid 80 through 83 removed outlier: 3.616A pdb=" N PHECP1 88 " --> pdb=" O ARGCP1 83 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLNCP1 110 " --> pdb=" O LEUCP1 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'CP1' and resid 129 through 130 Processing sheet with id=AA7, first strand: chain 'DP1' and resid 82 through 83 197 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1660 1.33 - 1.45: 1721 1.45 - 1.57: 3341 1.57 - 1.69: 151 1.69 - 1.81: 27 Bond restraints: 6900 Sorted by residual: bond pdb=" N GLUCP1 139 " pdb=" CA GLUCP1 139 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CB PROAP1 49 " pdb=" CG PROAP1 49 " ideal model delta sigma weight residual 1.506 1.478 0.028 3.90e-02 6.57e+02 5.17e-01 bond pdb=" N GLUBP4 417 " pdb=" CA GLUBP4 417 " ideal model delta sigma weight residual 1.457 1.467 -0.009 1.29e-02 6.01e+03 5.16e-01 bond pdb=" C1' GZN1 81 " pdb=" N9 GZN1 81 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 5.04e-01 bond pdb=" C1' AZN1 19 " pdb=" N9 AZN1 19 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 4.76e-01 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 9266 1.59 - 3.17: 376 3.17 - 4.76: 71 4.76 - 6.35: 16 6.35 - 7.94: 2 Bond angle restraints: 9731 Sorted by residual: angle pdb=" C LYSBP4 416 " pdb=" N GLUBP4 417 " pdb=" CA GLUBP4 417 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C3' GZN1 24 " pdb=" O3' GZN1 24 " pdb=" P CZN1 25 " ideal model delta sigma weight residual 119.70 123.44 -3.74 1.20e+00 6.94e-01 9.70e+00 angle pdb=" C3' GZN1 81 " pdb=" C2' GZN1 81 " pdb=" O2' GZN1 81 " ideal model delta sigma weight residual 109.80 115.15 -5.35 2.00e+00 2.50e-01 7.16e+00 angle pdb=" CB METBP4 344 " pdb=" CG METBP4 344 " pdb=" SD METBP4 344 " ideal model delta sigma weight residual 112.70 120.64 -7.94 3.00e+00 1.11e-01 7.00e+00 angle pdb=" O3' GZN1 9 " pdb=" C3' GZN1 9 " pdb=" C2' GZN1 9 " ideal model delta sigma weight residual 113.80 108.66 5.14 2.00e+00 2.50e-01 6.61e+00 ... (remaining 9726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.11: 3618 29.11 - 58.21: 257 58.21 - 87.32: 58 87.32 - 116.43: 0 116.43 - 145.53: 1 Dihedral angle restraints: 3934 sinusoidal: 2149 harmonic: 1785 Sorted by residual: dihedral pdb=" C4' AZN1 50 " pdb=" C3' AZN1 50 " pdb=" C2' AZN1 50 " pdb=" C1' AZN1 50 " ideal model delta sinusoidal sigma weight residual 36.34 -36.91 73.25 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' GZN1 22 " pdb=" C3' GZN1 22 " pdb=" C2' GZN1 22 " pdb=" C1' GZN1 22 " ideal model delta sinusoidal sigma weight residual 36.34 -36.78 73.13 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' GZN1 9 " pdb=" C3' GZN1 9 " pdb=" C2' GZN1 9 " pdb=" C1' GZN1 9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.65 73.00 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 3931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 910 0.062 - 0.124: 106 0.124 - 0.185: 6 0.185 - 0.247: 79 0.247 - 0.309: 34 Chirality restraints: 1135 Sorted by residual: chirality pdb=" C2' GZN1 81 " pdb=" C3' GZN1 81 " pdb=" O2' GZN1 81 " pdb=" C1' GZN1 81 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' GZN1 22 " pdb=" C4' GZN1 22 " pdb=" O3' GZN1 22 " pdb=" C2' GZN1 22 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C3' GZN1 59 " pdb=" C4' GZN1 59 " pdb=" O3' GZN1 59 " pdb=" C2' GZN1 59 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1132 not shown) Planarity restraints: 955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASPAP1 250 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PROAP1 251 " 0.086 5.00e-02 4.00e+02 pdb=" CA PROAP1 251 " -0.025 5.00e-02 4.00e+02 pdb=" CD PROAP1 251 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GZN1 81 " -0.026 2.00e-02 2.50e+03 1.14e-02 3.91e+00 pdb=" N9 GZN1 81 " 0.029 2.00e-02 2.50e+03 pdb=" C8 GZN1 81 " 0.002 2.00e-02 2.50e+03 pdb=" N7 GZN1 81 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GZN1 81 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GZN1 81 " -0.003 2.00e-02 2.50e+03 pdb=" O6 GZN1 81 " -0.007 2.00e-02 2.50e+03 pdb=" N1 GZN1 81 " -0.001 2.00e-02 2.50e+03 pdb=" C2 GZN1 81 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GZN1 81 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GZN1 81 " 0.003 2.00e-02 2.50e+03 pdb=" C4 GZN1 81 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AZN1 57 " -0.022 2.00e-02 2.50e+03 1.09e-02 3.28e+00 pdb=" N9 AZN1 57 " 0.027 2.00e-02 2.50e+03 pdb=" C8 AZN1 57 " 0.001 2.00e-02 2.50e+03 pdb=" N7 AZN1 57 " 0.000 2.00e-02 2.50e+03 pdb=" C5 AZN1 57 " -0.001 2.00e-02 2.50e+03 pdb=" C6 AZN1 57 " -0.004 2.00e-02 2.50e+03 pdb=" N6 AZN1 57 " -0.004 2.00e-02 2.50e+03 pdb=" N1 AZN1 57 " -0.002 2.00e-02 2.50e+03 pdb=" C2 AZN1 57 " 0.003 2.00e-02 2.50e+03 pdb=" N3 AZN1 57 " 0.006 2.00e-02 2.50e+03 pdb=" C4 AZN1 57 " -0.004 2.00e-02 2.50e+03 ... (remaining 952 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 374 2.73 - 3.27: 5552 3.27 - 3.81: 10382 3.81 - 4.36: 12762 4.36 - 4.90: 20749 Nonbonded interactions: 49819 Sorted by model distance: nonbonded pdb=" O2' GZN1 7 " pdb=" OP2 GZN1 62 " model vdw 2.184 3.040 nonbonded pdb=" O LEUCP1 144 " pdb=" OG1 THRCP1 149 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASPAP1 226 " pdb=" OH TYRAP1 301 " model vdw 2.248 3.040 nonbonded pdb=" NH1 ARGCP1 70 " pdb=" O GLUCP1 122 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THRAP1 287 " pdb=" O ASPDP1 163 " model vdw 2.269 3.040 ... (remaining 49814 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=0.00 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: 4.230 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.030 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.003 0.028 6900 Z= 0.124 Angle : 0.731 7.936 9731 Z= 0.330 Chirality : 0.085 0.309 1135 Planarity : 0.004 0.050 955 Dihedral : 18.819 145.533 2784 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.35), residues: 603 helix: 1.48 (0.43), residues: 169 sheet: 0.32 (0.46), residues: 152 loop : -1.55 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGCP1 472 TYR 0.017 0.001 TYRCP1 141 PHE 0.008 0.001 PHECP1 98 TRP 0.009 0.001 TRPDP1 76 HIS 0.002 0.000 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6900) covalent geometry : angle 0.73073 / 0.33 ( 9731) hydrogen bonds : bond 0.22421 / 15.07 ( 265) hydrogen bonds : angle 6.81221 / 4.50 ( 647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.196 Fit side-chains REVERT: DP1 92 LEU cc_start: 0.7764 (mp) cc_final: 0.7432 (mt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0911 time to fit residues: 5.8110 Evaluate side-chains 39 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.217979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167262 restraints weight = 6657.555| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.26 r_work: 0.3661 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 6900 Z= 0.202 Angle : 1.089 17.031 9731 Z= 0.459 Chirality : 0.098 0.983 1135 Planarity : 0.005 0.054 955 Dihedral : 17.071 151.869 1598 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.98 % Favored : 95.85 % Rotamer: Outliers : 0.38 % Allowed : 5.45 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.34), residues: 603 helix: 1.34 (0.42), residues: 175 sheet: 0.47 (0.46), residues: 142 loop : -1.65 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGCP1 472 TYR 0.024 0.002 TYRCP1 141 PHE 0.016 0.002 PHECP1 515 TRP 0.013 0.001 TRPCP1 82 HIS 0.002 0.001 HISAP1 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 ( 6900) covalent geometry : angle 1.08874 / 0.46 ( 9731) hydrogen bonds : bond 0.06247 / 4.30 ( 265) hydrogen bonds : angle 4.78518 / 3.22 ( 647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.150 Fit side-chains REVERT: DP1 92 LEU cc_start: 0.7488 (mp) cc_final: 0.7173 (mt) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.0920 time to fit residues: 4.9742 Evaluate side-chains 38 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 299 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.220253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.169950 restraints weight = 6584.959| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.16 r_work: 0.3690 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6900 Z= 0.140 Angle : 0.832 11.050 9731 Z= 0.361 Chirality : 0.075 0.601 1135 Planarity : 0.004 0.049 955 Dihedral : 16.869 150.872 1598 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 0.94 % Allowed : 7.89 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.34), residues: 603 helix: 1.47 (0.42), residues: 176 sheet: 0.60 (0.46), residues: 142 loop : -1.58 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGCP1 73 TYR 0.010 0.001 TYRCP1 141 PHE 0.012 0.001 PHEDP1 139 TRP 0.015 0.001 TRPCP1 82 HIS 0.002 0.000 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6900) covalent geometry : angle 0.83206 / 0.36 ( 9731) hydrogen bonds : bond 0.05581 / 3.95 ( 265) hydrogen bonds : angle 4.35299 / 2.93 ( 647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.201 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.0861 time to fit residues: 4.7796 Evaluate side-chains 40 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 299 VAL Chi-restraints excluded: chain DP1 residue 160 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.214722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.163485 restraints weight = 6679.790| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.22 r_work: 0.3623 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 6900 Z= 0.207 Angle : 0.912 11.918 9731 Z= 0.398 Chirality : 0.077 0.603 1135 Planarity : 0.005 0.052 955 Dihedral : 17.063 155.373 1598 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 0.94 % Allowed : 9.96 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.34), residues: 603 helix: 1.03 (0.41), residues: 182 sheet: 0.35 (0.45), residues: 145 loop : -1.67 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGCP1 73 TYR 0.013 0.002 TYRCP1 141 PHE 0.017 0.002 PHECP1 98 TRP 0.015 0.002 TRPCP1 82 HIS 0.003 0.001 HISDP1 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 ( 6900) covalent geometry : angle 0.91170 / 0.40 ( 9731) hydrogen bonds : bond 0.06582 / 4.73 ( 265) hydrogen bonds : angle 4.40723 / 2.96 ( 647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.181 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.0850 time to fit residues: 4.4037 Evaluate side-chains 37 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 299 VAL Chi-restraints excluded: chain CP1 residue 90 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.218680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167343 restraints weight = 6633.690| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.14 r_work: 0.3679 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6900 Z= 0.134 Angle : 0.784 10.400 9731 Z= 0.341 Chirality : 0.067 0.433 1135 Planarity : 0.004 0.046 955 Dihedral : 16.958 152.671 1598 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.64 % Favored : 95.19 % Rotamer: Outliers : 1.50 % Allowed : 11.65 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.34), residues: 603 helix: 1.23 (0.41), residues: 181 sheet: 0.44 (0.45), residues: 145 loop : -1.59 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGCP1 73 TYR 0.007 0.001 TYRBP4 369 PHE 0.014 0.001 PHEDP1 64 TRP 0.014 0.001 TRPCP1 82 HIS 0.002 0.000 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6900) covalent geometry : angle 0.78418 / 0.34 ( 9731) hydrogen bonds : bond 0.05414 / 3.92 ( 265) hydrogen bonds : angle 4.18004 / 2.80 ( 647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.207 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 0.0858 time to fit residues: 4.4776 Evaluate side-chains 39 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 299 VAL Chi-restraints excluded: chain BP4 residue 461 ASP Chi-restraints excluded: chain CP1 residue 33 LEU Chi-restraints excluded: chain CP1 residue 90 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.216553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164704 restraints weight = 6688.717| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.23 r_work: 0.3648 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6900 Z= 0.157 Angle : 0.811 10.131 9731 Z= 0.353 Chirality : 0.069 0.460 1135 Planarity : 0.004 0.046 955 Dihedral : 16.868 153.863 1598 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 1.88 % Allowed : 12.59 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.34), residues: 603 helix: 1.24 (0.41), residues: 182 sheet: 0.38 (0.45), residues: 145 loop : -1.60 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGCP1 73 TYR 0.008 0.001 TYRCP1 119 PHE 0.013 0.002 PHECP1 98 TRP 0.014 0.001 TRPCP1 82 HIS 0.002 0.001 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6900) covalent geometry : angle 0.81094 / 0.35 ( 9731) hydrogen bonds : bond 0.05761 / 4.19 ( 265) hydrogen bonds : angle 4.19199 / 2.82 ( 647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.189 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 39 average time/residue: 0.0774 time to fit residues: 4.2516 Evaluate side-chains 36 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 299 VAL Chi-restraints excluded: chain BP4 residue 461 ASP Chi-restraints excluded: chain CP1 residue 33 LEU Chi-restraints excluded: chain DP1 residue 140 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.217047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.165136 restraints weight = 6626.587| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.28 r_work: 0.3660 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6900 Z= 0.147 Angle : 0.787 9.807 9731 Z= 0.343 Chirality : 0.067 0.436 1135 Planarity : 0.004 0.045 955 Dihedral : 16.729 153.485 1598 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 1.50 % Allowed : 13.35 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.34), residues: 603 helix: 1.27 (0.41), residues: 182 sheet: 0.42 (0.45), residues: 145 loop : -1.57 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGCP1 83 TYR 0.008 0.001 TYRCP1 119 PHE 0.013 0.001 PHEDP1 139 TRP 0.013 0.001 TRPCP1 82 HIS 0.002 0.000 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6900) covalent geometry : angle 0.78719 / 0.34 ( 9731) hydrogen bonds : bond 0.05559 / 4.05 ( 265) hydrogen bonds : angle 4.12178 / 2.77 ( 647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.189 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.0927 time to fit residues: 4.7679 Evaluate side-chains 36 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 299 VAL Chi-restraints excluded: chain BP4 residue 461 ASP Chi-restraints excluded: chain CP1 residue 33 LEU Chi-restraints excluded: chain CP1 residue 446 LEU Chi-restraints excluded: chain DP1 residue 140 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 55 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.219579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171252 restraints weight = 6669.619| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.30 r_work: 0.3672 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6900 Z= 0.116 Angle : 0.750 9.321 9731 Z= 0.327 Chirality : 0.064 0.437 1135 Planarity : 0.004 0.042 955 Dihedral : 16.693 152.548 1598 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 1.32 % Allowed : 13.35 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.34), residues: 603 helix: 1.40 (0.41), residues: 182 sheet: 0.48 (0.45), residues: 145 loop : -1.53 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGCP1 73 TYR 0.009 0.001 TYRCP1 155 PHE 0.013 0.001 PHEDP1 139 TRP 0.013 0.001 TRPCP1 82 HIS 0.003 0.000 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 6900) covalent geometry : angle 0.75033 / 0.33 ( 9731) hydrogen bonds : bond 0.05083 / 3.72 ( 265) hydrogen bonds : angle 4.06966 / 2.74 ( 647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.198 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.0866 time to fit residues: 4.5644 Evaluate side-chains 38 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain BP4 residue 461 ASP Chi-restraints excluded: chain CP1 residue 33 LEU Chi-restraints excluded: chain CP1 residue 446 LEU Chi-restraints excluded: chain DP1 residue 140 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.217415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166581 restraints weight = 6681.005| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.21 r_work: 0.3656 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6900 Z= 0.143 Angle : 0.777 9.814 9731 Z= 0.339 Chirality : 0.066 0.456 1135 Planarity : 0.004 0.043 955 Dihedral : 16.584 153.349 1598 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.64 % Favored : 95.19 % Rotamer: Outliers : 1.32 % Allowed : 14.29 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.34), residues: 603 helix: 1.38 (0.41), residues: 182 sheet: 0.44 (0.45), residues: 145 loop : -1.54 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGCP1 73 TYR 0.008 0.001 TYRCP1 155 PHE 0.012 0.001 PHEDP1 139 TRP 0.014 0.001 TRPCP1 82 HIS 0.002 0.000 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6900) covalent geometry : angle 0.77651 / 0.34 ( 9731) hydrogen bonds : bond 0.05521 / 4.04 ( 265) hydrogen bonds : angle 4.07766 / 2.75 ( 647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.124 Fit side-chains REVERT: CP1 83 ARG cc_start: 0.7614 (mtt-85) cc_final: 0.7342 (mtt180) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.0795 time to fit residues: 3.9867 Evaluate side-chains 36 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain BP4 residue 461 ASP Chi-restraints excluded: chain CP1 residue 33 LEU Chi-restraints excluded: chain CP1 residue 446 LEU Chi-restraints excluded: chain DP1 residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 21 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.214902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.163544 restraints weight = 6600.656| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.28 r_work: 0.3615 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6900 Z= 0.174 Angle : 0.827 10.714 9731 Z= 0.362 Chirality : 0.070 0.475 1135 Planarity : 0.005 0.045 955 Dihedral : 16.594 154.959 1598 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 1.32 % Allowed : 14.47 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.34), residues: 603 helix: 1.25 (0.41), residues: 182 sheet: 0.38 (0.45), residues: 145 loop : -1.60 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGCP1 73 TYR 0.009 0.001 TYRCP1 119 PHE 0.015 0.002 PHECP1 98 TRP 0.013 0.001 TRPCP1 82 HIS 0.003 0.001 HISDP1 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 6900) covalent geometry : angle 0.82732 / 0.36 ( 9731) hydrogen bonds : bond 0.06038 / 4.40 ( 265) hydrogen bonds : angle 4.20945 / 2.84 ( 647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.151 Fit side-chains REVERT: CP1 83 ARG cc_start: 0.7578 (mtt-85) cc_final: 0.7272 (mtt180) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.0774 time to fit residues: 4.4945 Evaluate side-chains 40 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 3 VAL Chi-restraints excluded: chain AP1 residue 299 VAL Chi-restraints excluded: chain BP4 residue 461 ASP Chi-restraints excluded: chain CP1 residue 33 LEU Chi-restraints excluded: chain CP1 residue 446 LEU Chi-restraints excluded: chain DP1 residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.215411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166607 restraints weight = 6567.002| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.18 r_work: 0.3660 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6900 Z= 0.139 Angle : 0.782 10.241 9731 Z= 0.342 Chirality : 0.067 0.457 1135 Planarity : 0.004 0.043 955 Dihedral : 16.569 154.069 1598 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.64 % Favored : 95.19 % Rotamer: Outliers : 1.32 % Allowed : 14.29 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.34), residues: 603 helix: 1.32 (0.41), residues: 182 sheet: 0.44 (0.45), residues: 145 loop : -1.57 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGCP1 73 TYR 0.009 0.001 TYRCP1 155 PHE 0.013 0.001 PHEDP1 139 TRP 0.013 0.001 TRPCP1 82 HIS 0.002 0.001 HISBP4 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6900) covalent geometry : angle 0.78203 / 0.34 ( 9731) hydrogen bonds : bond 0.05479 / 4.00 ( 265) hydrogen bonds : angle 4.14735 / 2.79 ( 647) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1488.46 seconds wall clock time: 25 minutes 56.63 seconds (1556.63 seconds total)