Starting phenix.real_space_refine on Fri Aug 22 20:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqm_41508/08_2025/8tqm_41508_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqm_41508/08_2025/8tqm_41508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tqm_41508/08_2025/8tqm_41508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqm_41508/08_2025/8tqm_41508.map" model { file = "/net/cci-nas-00/data/ceres_data/8tqm_41508/08_2025/8tqm_41508_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqm_41508/08_2025/8tqm_41508_neut_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 4 5.49 5 S 39 5.16 5 C 4906 2.51 5 N 1087 2.21 5 O 1195 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7231 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6921 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 31, 'TRANS': 811} Chain breaks: 5 Chain: "A" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 310 Unusual residues: {'ERG': 1, 'PC1': 4, 'TGL': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Time building chain proxies: 1.49, per 1000 atoms: 0.21 Number of scatterers: 7231 At special positions: 0 Unit cell: (74.62, 102.83, 143.78, 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 39 16.00 P 4 15.00 O 1195 8.00 N 1087 7.00 C 4906 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: 0.53 Conformation dependent library (CDL) restraints added in 295.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 2 sheets defined 80.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 113 through 162 removed outlier: 4.629A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.582A pdb=" N SER A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 226 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.557A pdb=" N SER A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 522 removed outlier: 5.014A pdb=" N PHE A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 569 through 597 Proline residue: A 576 - end of helix removed outlier: 3.747A pdb=" N ASN A 593 " --> pdb=" O CYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 635 Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 672 through 700 removed outlier: 3.916A pdb=" N PHE A 676 " --> pdb=" O PRO A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 726 Processing helix chain 'A' and resid 727 through 756 removed outlier: 4.383A pdb=" N HIS A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 780 through 800 Processing helix chain 'A' and resid 802 through 823 Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 833 through 836 Processing helix chain 'A' and resid 844 through 849 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.631A pdb=" N GLN A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 936 Processing helix chain 'A' and resid 960 through 995 Processing helix chain 'A' and resid 998 through 1007 removed outlier: 3.720A pdb=" N VAL A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1029 through 1052 removed outlier: 4.537A pdb=" N LYS A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP A1046 " --> pdb=" O LYS A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 3.700A pdb=" N SER A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1137 Processing helix chain 'A' and resid 1137 through 1145 Processing helix chain 'A' and resid 1167 through 1195 removed outlier: 3.508A pdb=" N PHE A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A1194 " --> pdb=" O LYS A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1215 Processing helix chain 'A' and resid 1215 through 1230 removed outlier: 3.929A pdb=" N LEU A1224 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Proline residue: A1225 - end of helix Processing helix chain 'A' and resid 1265 through 1293 Processing sheet with id=AA1, first strand: chain 'A' and resid 838 through 842 Processing sheet with id=AA2, first strand: chain 'A' and resid 912 through 913 removed outlier: 3.963A pdb=" N LEU A 892 " --> pdb=" O VAL A 913 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1551 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: 0.83 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1401 1.33 - 1.45: 1788 1.45 - 1.57: 4156 1.57 - 1.69: 11 1.69 - 1.81: 67 Bond restraints: 7423 Sorted by residual: bond pdb=" C21 PC1 A1401 " pdb=" O21 PC1 A1401 " ideal model delta sigma weight residual 1.331 1.460 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C21 PC1 A1404 " pdb=" O21 PC1 A1404 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" OG3 TGL A1403 " pdb=" CC1 TGL A1403 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C21 PC1 A1402 " pdb=" O21 PC1 A1402 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C31 PC1 A1402 " pdb=" O31 PC1 A1402 " ideal model delta sigma weight residual 1.330 1.449 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 7418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 9939 4.20 - 8.41: 72 8.41 - 12.61: 9 12.61 - 16.82: 2 16.82 - 21.02: 1 Bond angle restraints: 10023 Sorted by residual: angle pdb=" N PC1 A1401 " pdb=" C12 PC1 A1401 " pdb=" C11 PC1 A1401 " ideal model delta sigma weight residual 115.31 136.33 -21.02 3.00e+00 1.11e-01 4.91e+01 angle pdb=" C LYS A 698 " pdb=" N ASN A 699 " pdb=" CA ASN A 699 " ideal model delta sigma weight residual 122.58 110.83 11.75 2.07e+00 2.33e-01 3.22e+01 angle pdb=" CAM Y01 A1406 " pdb=" CAY Y01 A1406 " pdb=" OAW Y01 A1406 " ideal model delta sigma weight residual 111.19 126.14 -14.95 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CA1 TGL A1403 " pdb=" CA2 TGL A1403 " pdb=" CA3 TGL A1403 " ideal model delta sigma weight residual 113.86 128.69 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA LYS A 804 " pdb=" C LYS A 804 " pdb=" N PRO A 805 " ideal model delta sigma weight residual 120.77 117.34 3.43 9.70e-01 1.06e+00 1.25e+01 ... (remaining 10018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 3933 13.88 - 27.77: 385 27.77 - 41.65: 132 41.65 - 55.54: 43 55.54 - 69.42: 13 Dihedral angle restraints: 4506 sinusoidal: 2011 harmonic: 2495 Sorted by residual: dihedral pdb=" CA ARG A 964 " pdb=" CB ARG A 964 " pdb=" CG ARG A 964 " pdb=" CD ARG A 964 " ideal model delta sinusoidal sigma weight residual -60.00 -113.15 53.15 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CA TYR A1222 " pdb=" C TYR A1222 " pdb=" N VAL A1223 " pdb=" CA VAL A1223 " ideal model delta harmonic sigma weight residual -180.00 -165.43 -14.57 0 5.00e+00 4.00e-02 8.49e+00 dihedral pdb=" CA LYS A 933 " pdb=" CB LYS A 933 " pdb=" CG LYS A 933 " pdb=" CD LYS A 933 " ideal model delta sinusoidal sigma weight residual 180.00 132.69 47.31 3 1.50e+01 4.44e-03 8.47e+00 ... (remaining 4503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1079 0.091 - 0.182: 39 0.182 - 0.272: 3 0.272 - 0.363: 1 0.363 - 0.454: 1 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CBH Y01 A1406 " pdb=" CAT Y01 A1406 " pdb=" CAZ Y01 A1406 " pdb=" CBF Y01 A1406 " both_signs ideal model delta sigma weight residual False -2.85 -2.40 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CBG Y01 A1406 " pdb=" CAQ Y01 A1406 " pdb=" CBD Y01 A1406 " pdb=" CBI Y01 A1406 " both_signs ideal model delta sigma weight residual False -2.33 -2.68 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CBF Y01 A1406 " pdb=" CAS Y01 A1406 " pdb=" CBD Y01 A1406 " pdb=" CBH Y01 A1406 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1120 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 671 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 672 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 672 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 672 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1000 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A1001 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1001 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1001 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 632 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C ILE A 632 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 632 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 633 " 0.010 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 16 2.36 - 2.99: 3984 2.99 - 3.63: 10885 3.63 - 4.26: 16156 4.26 - 4.90: 27239 Nonbonded interactions: 58280 Sorted by model distance: nonbonded pdb=" NH2 ARG A 734 " pdb=" NH2 ARG A 903 " model vdw 1.724 3.200 nonbonded pdb=" NH1 ARG A 734 " pdb=" NH1 ARG A 903 " model vdw 1.911 3.200 nonbonded pdb=" OG SER A1024 " pdb=" OD1 ASN A1029 " model vdw 2.118 3.040 nonbonded pdb=" ND2 ASN A 699 " pdb=" OE2 GLU A 808 " model vdw 2.212 3.120 nonbonded pdb=" NE2 HIS A 213 " pdb=" O1 ERG A1407 " model vdw 2.264 3.120 ... (remaining 58275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.030 Find NCS groups from input model: 0.020 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.007 0.129 7423 Z= 0.333 Angle : 0.919 21.021 10023 Z= 0.410 Chirality : 0.045 0.454 1123 Planarity : 0.004 0.047 1170 Dihedral : 13.425 69.421 2898 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.30), residues: 831 helix: 2.24 (0.20), residues: 651 sheet: -1.21 (1.11), residues: 22 loop : -1.24 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 597 TYR 0.016 0.001 TYR A 505 PHE 0.028 0.001 PHE A1171 TRP 0.016 0.001 TRP A 149 HIS 0.007 0.001 HIS A1049 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 7423) covalent geometry : angle 0.91883 (10023) hydrogen bonds : bond 0.10186 ( 521) hydrogen bonds : angle 5.26499 ( 1551) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.242 Fit side-chains REVERT: A 820 ARG cc_start: 0.8121 (tmm-80) cc_final: 0.7840 (ttp-110) REVERT: A 1219 MET cc_start: 0.7316 (mmm) cc_final: 0.6987 (tpt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0862 time to fit residues: 15.3740 Evaluate side-chains 92 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 20.0000 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 GLN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.194821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146642 restraints weight = 7827.300| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.81 r_work: 0.3031 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7423 Z= 0.132 Angle : 0.541 7.886 10023 Z= 0.275 Chirality : 0.038 0.153 1123 Planarity : 0.004 0.052 1170 Dihedral : 12.531 75.045 1278 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.26 % Allowed : 6.94 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.29), residues: 831 helix: 2.27 (0.20), residues: 660 sheet: -1.49 (1.08), residues: 22 loop : -1.04 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 702 TYR 0.029 0.001 TYR A 965 PHE 0.016 0.001 PHE A 614 TRP 0.011 0.001 TRP A 149 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7423) covalent geometry : angle 0.54098 (10023) hydrogen bonds : bond 0.04256 ( 521) hydrogen bonds : angle 4.79104 ( 1551) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.248 Fit side-chains REVERT: A 599 TYR cc_start: 0.8094 (m-80) cc_final: 0.7821 (m-80) REVERT: A 816 LYS cc_start: 0.8657 (tttt) cc_final: 0.7837 (mttm) REVERT: A 820 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.8166 (ttp-110) REVERT: A 835 THR cc_start: 0.9190 (t) cc_final: 0.8806 (m) REVERT: A 963 LEU cc_start: 0.8343 (mm) cc_final: 0.7971 (mm) REVERT: A 1047 ILE cc_start: 0.7084 (mt) cc_final: 0.6831 (mt) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.0802 time to fit residues: 11.1007 Evaluate side-chains 91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.192484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146541 restraints weight = 7717.252| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.83 r_work: 0.3071 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7423 Z= 0.182 Angle : 0.563 8.141 10023 Z= 0.285 Chirality : 0.040 0.149 1123 Planarity : 0.004 0.053 1170 Dihedral : 12.487 80.054 1278 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.65 % Allowed : 9.16 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.29), residues: 831 helix: 2.11 (0.20), residues: 662 sheet: -1.62 (1.10), residues: 22 loop : -1.14 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.027 0.001 TYR A 965 PHE 0.015 0.001 PHE A 614 TRP 0.010 0.001 TRP A 662 HIS 0.005 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 7423) covalent geometry : angle 0.56257 (10023) hydrogen bonds : bond 0.04284 ( 521) hydrogen bonds : angle 4.78805 ( 1551) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.157 Fit side-chains REVERT: A 175 ILE cc_start: 0.8644 (mm) cc_final: 0.8197 (mt) REVERT: A 816 LYS cc_start: 0.8518 (tttt) cc_final: 0.7647 (mttm) REVERT: A 835 THR cc_start: 0.9099 (t) cc_final: 0.8723 (m) REVERT: A 1047 ILE cc_start: 0.7063 (mt) cc_final: 0.6819 (mt) outliers start: 5 outliers final: 1 residues processed: 96 average time/residue: 0.0789 time to fit residues: 10.4672 Evaluate side-chains 84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.192120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.140141 restraints weight = 7829.098| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.90 r_work: 0.2953 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7423 Z= 0.141 Angle : 0.514 7.357 10023 Z= 0.261 Chirality : 0.038 0.141 1123 Planarity : 0.004 0.055 1170 Dihedral : 12.283 80.730 1278 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.05 % Allowed : 10.60 % Favored : 88.35 % 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: 2.30 (0.29), residues: 831 helix: 2.17 (0.20), residues: 662 sheet: -1.53 (1.12), residues: 22 loop : -1.03 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 225 TYR 0.023 0.001 TYR A 965 PHE 0.013 0.001 PHE A 614 TRP 0.011 0.001 TRP A 662 HIS 0.004 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7423) covalent geometry : angle 0.51363 (10023) hydrogen bonds : bond 0.03949 ( 521) hydrogen bonds : angle 4.66481 ( 1551) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.285 Fit side-chains REVERT: A 175 ILE cc_start: 0.8681 (mm) cc_final: 0.8260 (mt) REVERT: A 816 LYS cc_start: 0.8627 (tttt) cc_final: 0.7837 (mttm) REVERT: A 1015 VAL cc_start: 0.7905 (t) cc_final: 0.7459 (m) REVERT: A 1106 ASP cc_start: 0.7500 (m-30) cc_final: 0.6801 (m-30) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.0668 time to fit residues: 8.6190 Evaluate side-chains 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 1029 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 75 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.191283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.138204 restraints weight = 7788.223| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.91 r_work: 0.2922 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7423 Z= 0.156 Angle : 0.521 7.438 10023 Z= 0.265 Chirality : 0.039 0.143 1123 Planarity : 0.004 0.054 1170 Dihedral : 12.294 80.595 1278 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.31 % Allowed : 11.26 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.29), residues: 831 helix: 2.16 (0.20), residues: 662 sheet: -1.75 (1.07), residues: 22 loop : -1.02 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.024 0.001 TYR A 965 PHE 0.013 0.001 PHE A 614 TRP 0.011 0.001 TRP A 662 HIS 0.005 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7423) covalent geometry : angle 0.52052 (10023) hydrogen bonds : bond 0.03990 ( 521) hydrogen bonds : angle 4.67746 ( 1551) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.218 Fit side-chains REVERT: A 175 ILE cc_start: 0.8679 (mm) cc_final: 0.8294 (mt) REVERT: A 816 LYS cc_start: 0.8595 (tttt) cc_final: 0.7749 (mttm) REVERT: A 1015 VAL cc_start: 0.7923 (t) cc_final: 0.7479 (m) REVERT: A 1106 ASP cc_start: 0.7462 (m-30) cc_final: 0.6805 (m-30) outliers start: 10 outliers final: 5 residues processed: 92 average time/residue: 0.0668 time to fit residues: 8.7950 Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 1029 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.195168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.149101 restraints weight = 7738.988| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.63 r_work: 0.2988 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7423 Z= 0.127 Angle : 0.491 7.092 10023 Z= 0.250 Chirality : 0.037 0.140 1123 Planarity : 0.004 0.055 1170 Dihedral : 11.940 82.063 1278 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.79 % Allowed : 12.04 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.29), residues: 831 helix: 2.25 (0.20), residues: 663 sheet: -1.81 (1.07), residues: 22 loop : -1.06 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.022 0.001 TYR A 965 PHE 0.011 0.001 PHE A 614 TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7423) covalent geometry : angle 0.49067 (10023) hydrogen bonds : bond 0.03755 ( 521) hydrogen bonds : angle 4.56118 ( 1551) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.269 Fit side-chains REVERT: A 175 ILE cc_start: 0.8693 (mm) cc_final: 0.8311 (mt) REVERT: A 505 TYR cc_start: 0.8117 (m-10) cc_final: 0.7788 (m-10) REVERT: A 737 LEU cc_start: 0.7919 (mp) cc_final: 0.7717 (mt) REVERT: A 816 LYS cc_start: 0.8558 (tttt) cc_final: 0.7736 (mttm) REVERT: A 1015 VAL cc_start: 0.7879 (t) cc_final: 0.7432 (m) REVERT: A 1106 ASP cc_start: 0.7411 (m-30) cc_final: 0.6765 (m-30) REVERT: A 1266 MET cc_start: 0.5141 (ppp) cc_final: 0.4726 (ppp) outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 0.0662 time to fit residues: 8.7243 Evaluate side-chains 91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.0470 chunk 18 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN A 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.193385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.142025 restraints weight = 7792.507| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.90 r_work: 0.2950 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7423 Z= 0.127 Angle : 0.487 7.269 10023 Z= 0.250 Chirality : 0.038 0.140 1123 Planarity : 0.004 0.055 1170 Dihedral : 11.743 82.444 1278 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.65 % Allowed : 12.96 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.29), residues: 831 helix: 2.29 (0.20), residues: 663 sheet: -1.85 (1.04), residues: 22 loop : -1.01 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.021 0.001 TYR A 965 PHE 0.012 0.001 PHE A 614 TRP 0.011 0.001 TRP A 662 HIS 0.004 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7423) covalent geometry : angle 0.48680 (10023) hydrogen bonds : bond 0.03742 ( 521) hydrogen bonds : angle 4.50711 ( 1551) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.198 Fit side-chains REVERT: A 175 ILE cc_start: 0.8687 (mm) cc_final: 0.8320 (mt) REVERT: A 505 TYR cc_start: 0.8086 (m-10) cc_final: 0.7760 (m-10) REVERT: A 816 LYS cc_start: 0.8558 (tttt) cc_final: 0.7708 (mttm) REVERT: A 944 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7136 (tm-30) REVERT: A 963 LEU cc_start: 0.8197 (mm) cc_final: 0.7937 (mm) REVERT: A 1015 VAL cc_start: 0.7866 (t) cc_final: 0.7412 (m) REVERT: A 1266 MET cc_start: 0.5027 (ppp) cc_final: 0.4629 (ppp) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.0670 time to fit residues: 8.6157 Evaluate side-chains 88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 ASN A 932 ASN A 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.192325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.142077 restraints weight = 7819.742| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.08 r_work: 0.2902 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 0.037 7423 Z= 0.140 Angle : 0.506 7.338 10023 Z= 0.260 Chirality : 0.038 0.140 1123 Planarity : 0.004 0.054 1170 Dihedral : 11.764 84.144 1278 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.79 % Allowed : 13.61 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.29), residues: 831 helix: 2.23 (0.20), residues: 663 sheet: -1.80 (1.06), residues: 22 loop : -1.03 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1126 TYR 0.022 0.001 TYR A 965 PHE 0.012 0.001 PHE A 614 TRP 0.011 0.001 TRP A 662 HIS 0.004 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7423) covalent geometry : angle 0.50636 (10023) hydrogen bonds : bond 0.03863 ( 521) hydrogen bonds : angle 4.54879 ( 1551) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.169 Fit side-chains REVERT: A 175 ILE cc_start: 0.8733 (mm) cc_final: 0.8379 (mt) REVERT: A 505 TYR cc_start: 0.8154 (m-10) cc_final: 0.7871 (m-10) REVERT: A 710 ARG cc_start: 0.7689 (ttm110) cc_final: 0.7488 (ttm-80) REVERT: A 737 LEU cc_start: 0.7899 (mp) cc_final: 0.7646 (mt) REVERT: A 816 LYS cc_start: 0.8613 (tttt) cc_final: 0.7766 (mttm) REVERT: A 963 LEU cc_start: 0.8213 (mm) cc_final: 0.7967 (mm) REVERT: A 1266 MET cc_start: 0.5090 (ppp) cc_final: 0.4719 (ppp) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.0646 time to fit residues: 8.2275 Evaluate side-chains 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 1218 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 36 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.192205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.141242 restraints weight = 7761.985| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.09 r_work: 0.2947 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7423 Z= 0.125 Angle : 0.489 6.147 10023 Z= 0.252 Chirality : 0.038 0.139 1123 Planarity : 0.004 0.055 1170 Dihedral : 11.603 89.221 1278 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.39 % Allowed : 13.61 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.29), residues: 831 helix: 2.25 (0.20), residues: 663 sheet: -1.78 (1.06), residues: 22 loop : -1.01 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1126 TYR 0.020 0.001 TYR A 965 PHE 0.012 0.001 PHE A 614 TRP 0.011 0.001 TRP A 662 HIS 0.002 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7423) covalent geometry : angle 0.48870 (10023) hydrogen bonds : bond 0.03732 ( 521) hydrogen bonds : angle 4.49760 ( 1551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.249 Fit side-chains REVERT: A 175 ILE cc_start: 0.8744 (mm) cc_final: 0.8388 (mt) REVERT: A 505 TYR cc_start: 0.8159 (m-10) cc_final: 0.7892 (m-10) REVERT: A 737 LEU cc_start: 0.7910 (mp) cc_final: 0.7654 (mt) REVERT: A 816 LYS cc_start: 0.8611 (tttt) cc_final: 0.7779 (mttm) REVERT: A 963 LEU cc_start: 0.8189 (mm) cc_final: 0.7972 (mm) REVERT: A 1266 MET cc_start: 0.5059 (ppp) cc_final: 0.4693 (ppp) outliers start: 3 outliers final: 3 residues processed: 85 average time/residue: 0.0647 time to fit residues: 8.0299 Evaluate side-chains 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 0.0570 chunk 78 optimal weight: 5.9990 overall best weight: 0.5912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 859 ASN A 932 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.192491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.142340 restraints weight = 7773.733| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.06 r_work: 0.3071 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7423 Z= 0.132 Angle : 0.498 6.303 10023 Z= 0.258 Chirality : 0.038 0.139 1123 Planarity : 0.004 0.054 1170 Dihedral : 11.522 84.877 1278 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.92 % Allowed : 13.61 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.29), residues: 831 helix: 2.22 (0.20), residues: 663 sheet: -1.76 (1.09), residues: 22 loop : -1.04 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 964 TYR 0.020 0.001 TYR A 965 PHE 0.012 0.001 PHE A 614 TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7423) covalent geometry : angle 0.49840 (10023) hydrogen bonds : bond 0.03768 ( 521) hydrogen bonds : angle 4.50293 ( 1551) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.213 Fit side-chains REVERT: A 175 ILE cc_start: 0.8762 (mm) cc_final: 0.8407 (mt) REVERT: A 505 TYR cc_start: 0.8138 (m-10) cc_final: 0.7882 (m-10) REVERT: A 737 LEU cc_start: 0.7901 (mp) cc_final: 0.7639 (mt) REVERT: A 816 LYS cc_start: 0.8581 (tttt) cc_final: 0.7737 (mttm) REVERT: A 963 LEU cc_start: 0.8159 (mm) cc_final: 0.7959 (mm) REVERT: A 1219 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6317 (mmt) REVERT: A 1266 MET cc_start: 0.5086 (ppp) cc_final: 0.4709 (ppp) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.0761 time to fit residues: 9.3380 Evaluate side-chains 89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 1218 HIS Chi-restraints excluded: chain A residue 1219 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 0.4980 chunk 5 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.192169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.140914 restraints weight = 7813.615| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.05 r_work: 0.3071 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7423 Z= 0.138 Angle : 0.507 6.237 10023 Z= 0.263 Chirality : 0.038 0.139 1123 Planarity : 0.004 0.054 1170 Dihedral : 11.466 85.259 1278 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.65 % Allowed : 14.14 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.29), residues: 831 helix: 2.22 (0.20), residues: 663 sheet: -1.83 (1.10), residues: 22 loop : -1.01 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 710 TYR 0.021 0.001 TYR A 965 PHE 0.022 0.001 PHE A 999 TRP 0.011 0.001 TRP A 662 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7423) covalent geometry : angle 0.50660 (10023) hydrogen bonds : bond 0.03786 ( 521) hydrogen bonds : angle 4.51365 ( 1551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.94 seconds wall clock time: 31 minutes 11.97 seconds (1871.97 seconds total)