Starting phenix.real_space_refine on Fri Sep 11 02:56:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.map" model { file = "/net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7odf_12827/09_2026/7odf_12827.cif" } resolution = 2.66 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= 1.000 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: 7 Type Number sf(0) Gaussians Ni 1 6.56 5 Zn 1 6.06 5 P 78 5.49 5 S 16 5.16 5 C 4068 2.51 5 N 1216 2.21 5 O 1467 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: 6847 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5205 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 30, 'TRANS': 672} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 4, 'GLU:plan': 26, 'ARG:plan': 7, 'ASN:plan1': 15, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 256 Chain: "E" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 919 Classifications: {'RNAv2': 43} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 36} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' NI': 1, ' ZN': 1} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4879 SG CYS A 680 72.409 39.562 72.141 1.00106.49 S ATOM 4900 SG CYS A 683 76.785 37.518 72.841 1.00112.67 S ATOM 5015 SG CYS A 701 74.842 39.676 74.908 1.00117.90 S Time building chain proxies: 1.30, per 1000 atoms: 0.19 Number of scatterers: 6847 At special positions: 0 Unit cell: (84.864, 98.176, 115.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ni 1 28.00 S 16 16.00 P 78 15.00 O 1467 8.00 N 1216 7.00 C 4068 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: 0.63 Conformation dependent library (CDL) restraints added in 387.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 701 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 683 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 680 " 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 50.2% alpha, 8.1% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.779A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 35 removed outlier: 3.631A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.571A pdb=" N SER A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 121 through 160 removed outlier: 3.593A pdb=" N THR A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.618A pdb=" N GLU A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 445 through 473 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 501 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.529A pdb=" N SER A 512 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 513 " --> pdb=" O TRP A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 561 through 579 Processing helix chain 'A' and resid 580 through 608 removed outlier: 3.795A pdb=" N LYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.588A pdb=" N PHE A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 710 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.238A pdb=" N ASN A 61 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 330 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 65 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP A 328 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 442 removed outlier: 3.538A pdb=" N VAL A 407 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 408 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 616 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 410 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLU A 618 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N VAL A 412 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A 667 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AA4, first strand: chain 'A' and resid 695 through 697 269 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1905 1.34 - 1.46: 1707 1.46 - 1.58: 3356 1.58 - 1.70: 152 1.70 - 1.82: 22 Bond restraints: 7142 Sorted by residual: bond pdb=" C3' DT E 22 " pdb=" C2' DT E 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.93e+00 bond pdb=" O3' DG C 1 " pdb=" P DG C 2 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.20e-02 6.94e+03 5.80e+00 bond pdb=" O4' DC E 14 " pdb=" C1' DC E 14 " ideal model delta sigma weight residual 1.420 1.396 0.024 1.10e-02 8.26e+03 4.63e+00 bond pdb=" C1' DC E 6 " pdb=" N1 DC E 6 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.49e+00 ... (remaining 7137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 9545 1.27 - 2.53: 363 2.53 - 3.80: 121 3.80 - 5.06: 22 5.06 - 6.33: 5 Bond angle restraints: 10056 Sorted by residual: angle pdb=" N3 DT G 6 " pdb=" C4 DT G 6 " pdb=" O4 DT G 6 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT E 18 " pdb=" C4 DT E 18 " pdb=" O4 DT E 18 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E 22 " pdb=" C4 DT E 22 " pdb=" O4 DT E 22 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT G 2 " pdb=" C4 DT G 2 " pdb=" O4 DT G 2 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT G 5 " pdb=" C4 DT G 5 " pdb=" O4 DT G 5 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 10051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.08: 3757 28.08 - 56.17: 256 56.17 - 84.25: 53 84.25 - 112.33: 0 112.33 - 140.42: 1 Dihedral angle restraints: 4067 sinusoidal: 2019 harmonic: 2048 Sorted by residual: dihedral pdb=" C4' U F 7 " pdb=" C3' U F 7 " pdb=" C2' U F 7 " pdb=" C1' U F 7 " ideal model delta sinusoidal sigma weight residual 36.34 -37.78 74.13 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' A F 26 " pdb=" C3' A F 26 " pdb=" C2' A F 26 " pdb=" C1' A F 26 " ideal model delta sinusoidal sigma weight residual 36.35 -36.78 73.12 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' A F 2 " pdb=" C3' A F 2 " pdb=" C2' A F 2 " pdb=" C1' A F 2 " ideal model delta sinusoidal sigma weight residual 36.34 -36.13 72.48 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 971 0.058 - 0.116: 145 0.116 - 0.173: 14 0.173 - 0.231: 34 0.231 - 0.289: 21 Chirality restraints: 1185 Sorted by residual: chirality pdb=" C2' A F 26 " pdb=" C3' A F 26 " pdb=" O2' A F 26 " pdb=" C1' A F 26 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' U F 7 " pdb=" C3' U F 7 " pdb=" O2' U F 7 " pdb=" C1' U F 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C3' U F 7 " pdb=" C4' U F 7 " pdb=" O3' U F 7 " pdb=" C2' U F 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1182 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 587 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C LYS A 587 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A 587 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 588 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 218 " 0.013 2.00e-02 2.50e+03 1.44e-02 4.13e+00 pdb=" CG TYR A 218 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 218 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 218 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 218 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 218 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 218 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 218 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 337 " -0.016 2.00e-02 2.50e+03 1.24e-02 3.09e+00 pdb=" CG TYR A 337 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 337 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 337 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 337 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 337 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 337 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 337 " 0.001 2.00e-02 2.50e+03 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 32 2.54 - 3.13: 5116 3.13 - 3.72: 11540 3.72 - 4.31: 16290 4.31 - 4.90: 25151 Nonbonded interactions: 58129 Sorted by model distance: nonbonded pdb=" OD1 ASP A 413 " pdb="NI NI A 801 " model vdw 1.952 2.180 nonbonded pdb=" OG1 THR A 60 " pdb=" O VAL A 372 " model vdw 2.198 3.040 nonbonded pdb=" O ASN A 275 " pdb=" O2' G F 14 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 296 " pdb=" OP2 C F 19 " model vdw 2.239 3.040 nonbonded pdb=" O LYS A 400 " pdb=" OG SER A 403 " model vdw 2.336 3.040 ... (remaining 58124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.009 0.661 7145 Z= 0.376 Angle : 0.641 6.331 10056 Z= 0.405 Chirality : 0.064 0.289 1185 Planarity : 0.003 0.032 1014 Dihedral : 17.873 140.418 2743 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.32), residues: 699 helix: 2.00 (0.29), residues: 315 sheet: 0.19 (0.61), residues: 70 loop : 0.20 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.033 0.002 TYR A 218 PHE 0.020 0.001 PHE A 341 TRP 0.010 0.001 TRP A 636 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.27 ( 7142) covalent geometry : angle 0.64092 / 0.41 (10056) hydrogen bonds : bond 0.19328 / 13.18 ( 339) hydrogen bonds : angle 6.99053 / 5.12 ( 892) metal coordination : bond 0.38155 / 20.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.255 Fit side-chains REVERT: A 621 ASP cc_start: 0.7918 (t70) cc_final: 0.7329 (t70) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.5311 time to fit residues: 41.6957 Evaluate side-chains 46 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.140744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106543 restraints weight = 9024.607| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.98 r_work: 0.3221 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7145 Z= 0.223 Angle : 0.941 19.930 10056 Z= 0.422 Chirality : 0.082 1.227 1185 Planarity : 0.004 0.031 1014 Dihedral : 17.647 141.667 1653 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.57 % Allowed : 6.85 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.32), residues: 699 helix: 2.24 (0.29), residues: 312 sheet: -0.33 (0.58), residues: 82 loop : 0.26 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 287 TYR 0.022 0.002 TYR A 218 PHE 0.025 0.002 PHE A 488 TRP 0.013 0.001 TRP A 636 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 ( 7142) covalent geometry : angle 0.94075 / 0.42 (10056) hydrogen bonds : bond 0.04742 / 3.23 ( 339) hydrogen bonds : angle 4.59707 / 3.53 ( 892) metal coordination : bond 0.02839 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.197 Fit side-chains REVERT: A 391 ARG cc_start: 0.8607 (ptp-170) cc_final: 0.8375 (ptp-170) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.4702 time to fit residues: 28.6779 Evaluate side-chains 54 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 23 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109752 restraints weight = 9070.597| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.99 r_work: 0.3273 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7145 Z= 0.148 Angle : 0.700 13.987 10056 Z= 0.334 Chirality : 0.062 0.826 1185 Planarity : 0.003 0.029 1014 Dihedral : 17.585 140.036 1653 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.57 % Allowed : 9.39 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.32), residues: 699 helix: 2.38 (0.29), residues: 312 sheet: -0.40 (0.58), residues: 82 loop : 0.31 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 594 TYR 0.018 0.001 TYR A 218 PHE 0.016 0.001 PHE A 488 TRP 0.012 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 7142) covalent geometry : angle 0.69952 / 0.33 (10056) hydrogen bonds : bond 0.04276 / 2.89 ( 339) hydrogen bonds : angle 4.24907 / 3.25 ( 892) metal coordination : bond 0.00601 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 621 ASP cc_start: 0.8246 (t70) cc_final: 0.7615 (t70) outliers start: 8 outliers final: 7 residues processed: 59 average time/residue: 0.4627 time to fit residues: 29.2186 Evaluate side-chains 55 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 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 = 0.3817 r_free = 0.3817 target = 0.143436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108961 restraints weight = 9629.184| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.15 r_work: 0.3294 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7145 Z= 0.152 Angle : 0.652 8.378 10056 Z= 0.316 Chirality : 0.055 0.452 1185 Planarity : 0.003 0.044 1014 Dihedral : 17.604 148.147 1653 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.54 % Allowed : 9.20 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.32), residues: 699 helix: 2.32 (0.29), residues: 316 sheet: -0.47 (0.58), residues: 82 loop : 0.34 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.026 0.001 TYR A 218 PHE 0.012 0.001 PHE A 488 TRP 0.011 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 7142) covalent geometry : angle 0.65234 / 0.32 (10056) hydrogen bonds : bond 0.03835 / 2.55 ( 339) hydrogen bonds : angle 4.08724 / 3.12 ( 892) metal coordination : bond 0.00349 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 621 ASP cc_start: 0.8085 (t70) cc_final: 0.7417 (t70) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.3855 time to fit residues: 26.2080 Evaluate side-chains 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.144540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111369 restraints weight = 9722.108| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.06 r_work: 0.3385 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7145 Z= 0.152 Angle : 0.632 7.885 10056 Z= 0.308 Chirality : 0.054 0.441 1185 Planarity : 0.003 0.029 1014 Dihedral : 17.625 148.824 1653 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.54 % Allowed : 11.15 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.32), residues: 699 helix: 2.32 (0.29), residues: 316 sheet: -0.48 (0.58), residues: 82 loop : 0.33 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.026 0.001 TYR A 218 PHE 0.010 0.001 PHE A 640 TRP 0.010 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 7142) covalent geometry : angle 0.63220 / 0.31 (10056) hydrogen bonds : bond 0.03840 / 2.59 ( 339) hydrogen bonds : angle 4.03631 / 3.09 ( 892) metal coordination : bond 0.00125 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 621 ASP cc_start: 0.8214 (t70) cc_final: 0.7560 (t70) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.4590 time to fit residues: 29.5126 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103623 restraints weight = 9615.386| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.03 r_work: 0.3285 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 7145 Z= 0.341 Angle : 0.779 9.214 10056 Z= 0.374 Chirality : 0.062 0.564 1185 Planarity : 0.004 0.028 1014 Dihedral : 17.855 147.791 1653 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.94 % Allowed : 10.96 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.32), residues: 699 helix: 2.18 (0.29), residues: 313 sheet: -0.15 (0.64), residues: 74 loop : 0.26 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.033 0.002 TYR A 218 PHE 0.018 0.002 PHE A 341 TRP 0.014 0.002 TRP A 72 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.34 ( 7142) covalent geometry : angle 0.77941 / 0.37 (10056) hydrogen bonds : bond 0.04859 / 3.29 ( 339) hydrogen bonds : angle 4.28020 / 3.26 ( 892) metal coordination : bond 0.00322 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8149 (tp) REVERT: A 621 ASP cc_start: 0.8264 (t70) cc_final: 0.7636 (t70) outliers start: 15 outliers final: 9 residues processed: 61 average time/residue: 0.4391 time to fit residues: 28.7391 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN ** A 672 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 = 0.3847 r_free = 0.3847 target = 0.144181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111183 restraints weight = 9572.665| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.04 r_work: 0.3381 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7145 Z= 0.136 Angle : 0.635 8.214 10056 Z= 0.309 Chirality : 0.054 0.468 1185 Planarity : 0.003 0.028 1014 Dihedral : 17.862 152.769 1653 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.35 % Allowed : 13.11 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.32), residues: 699 helix: 2.39 (0.29), residues: 310 sheet: -0.33 (0.61), residues: 74 loop : 0.35 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.023 0.001 TYR A 218 PHE 0.013 0.001 PHE A 341 TRP 0.012 0.001 TRP A 636 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 7142) covalent geometry : angle 0.63514 / 0.31 (10056) hydrogen bonds : bond 0.03703 / 2.50 ( 339) hydrogen bonds : angle 4.07299 / 3.13 ( 892) metal coordination : bond 0.00067 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8088 (tp) REVERT: A 621 ASP cc_start: 0.8248 (t70) cc_final: 0.7583 (t70) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.3685 time to fit residues: 24.0390 Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 567 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111520 restraints weight = 9741.892| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.06 r_work: 0.3383 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7145 Z= 0.143 Angle : 0.623 8.762 10056 Z= 0.303 Chirality : 0.053 0.401 1185 Planarity : 0.003 0.030 1014 Dihedral : 17.719 148.714 1653 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.54 % Allowed : 13.70 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.32), residues: 699 helix: 2.48 (0.29), residues: 310 sheet: -0.63 (0.57), residues: 82 loop : 0.30 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 594 TYR 0.028 0.001 TYR A 218 PHE 0.010 0.001 PHE A 640 TRP 0.010 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 7142) covalent geometry : angle 0.62270 / 0.30 (10056) hydrogen bonds : bond 0.03635 / 2.43 ( 339) hydrogen bonds : angle 4.02085 / 3.08 ( 892) metal coordination : bond 0.00269 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8068 (tp) outliers start: 13 outliers final: 11 residues processed: 59 average time/residue: 0.4711 time to fit residues: 29.6162 Evaluate side-chains 59 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN ** A 672 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 = 0.3864 r_free = 0.3864 target = 0.145725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112792 restraints weight = 9648.339| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.06 r_work: 0.3398 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7145 Z= 0.125 Angle : 0.609 7.636 10056 Z= 0.298 Chirality : 0.052 0.375 1185 Planarity : 0.003 0.033 1014 Dihedral : 17.666 148.090 1653 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.15 % Allowed : 14.48 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.32), residues: 699 helix: 2.52 (0.29), residues: 310 sheet: -0.66 (0.57), residues: 82 loop : 0.31 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 691 TYR 0.029 0.001 TYR A 218 PHE 0.014 0.001 PHE A 488 TRP 0.010 0.001 TRP A 675 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 7142) covalent geometry : angle 0.60919 / 0.30 (10056) hydrogen bonds : bond 0.03546 / 2.39 ( 339) hydrogen bonds : angle 3.99416 / 3.06 ( 892) metal coordination : bond 0.00119 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8644 (m-80) cc_final: 0.8435 (m-80) REVERT: A 610 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8024 (tp) outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 0.4002 time to fit residues: 24.5907 Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.0170 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 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 = 0.3865 r_free = 0.3865 target = 0.145247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111911 restraints weight = 9659.395| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.04 r_work: 0.3414 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7145 Z= 0.124 Angle : 0.606 8.854 10056 Z= 0.296 Chirality : 0.051 0.355 1185 Planarity : 0.003 0.033 1014 Dihedral : 17.565 145.864 1653 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.96 % Allowed : 14.29 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.32), residues: 699 helix: 2.44 (0.29), residues: 310 sheet: -0.63 (0.57), residues: 82 loop : 0.34 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 492 TYR 0.029 0.001 TYR A 218 PHE 0.011 0.001 PHE A 249 TRP 0.010 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 7142) covalent geometry : angle 0.60580 / 0.30 (10056) hydrogen bonds : bond 0.03550 / 2.38 ( 339) hydrogen bonds : angle 3.93083 / 3.01 ( 892) metal coordination : bond 0.00066 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 610 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 633 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8002 (m-30) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.4226 time to fit residues: 25.4494 Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 60 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 23 optimal weight: 0.0030 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 66 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 overall best weight: 1.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109571 restraints weight = 9657.152| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.05 r_work: 0.3363 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7145 Z= 0.194 Angle : 0.638 7.972 10056 Z= 0.310 Chirality : 0.053 0.408 1185 Planarity : 0.003 0.034 1014 Dihedral : 17.629 145.427 1653 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.35 % Allowed : 14.09 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.32), residues: 699 helix: 2.31 (0.29), residues: 316 sheet: -0.29 (0.61), residues: 74 loop : 0.41 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 492 TYR 0.036 0.002 TYR A 218 PHE 0.011 0.001 PHE A 640 TRP 0.011 0.001 TRP A 675 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 7142) covalent geometry : angle 0.63792 / 0.31 (10056) hydrogen bonds : bond 0.03851 / 2.59 ( 339) hydrogen bonds : angle 3.99443 / 3.05 ( 892) metal coordination : bond 0.00172 / 0.09 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.12 seconds wall clock time: 45 minutes 53.13 seconds (2753.13 seconds total)