Starting phenix.real_space_refine on Tue Mar 3 16:22:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7odf_12827/03_2026/7odf_12827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7odf_12827/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7odf_12827/03_2026/7odf_12827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7odf_12827/03_2026/7odf_12827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7odf_12827/03_2026/7odf_12827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7odf_12827/03_2026/7odf_12827.map" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: 1.72, per 1000 atoms: 0.25 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: 0.62 Conformation dependent library (CDL) restraints added in 228.3 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: 1.12 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: 1.10 Time building geometry restraints manager: 0.85 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=" O3' DG C 1 " pdb=" P DG C 2 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.50e-02 4.44e+03 3.71e+00 bond pdb=" CG LEU A 336 " pdb=" CD1 LEU A 336 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CD GLU A 591 " pdb=" OE1 GLU A 591 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.31e+00 bond pdb=" CG GLU A 591 " pdb=" CD GLU A 591 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 9.09e-01 bond pdb=" O4' DC E 14 " pdb=" C1' DC E 14 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 7.80e-01 ... (remaining 7137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 9786 1.27 - 2.53: 217 2.53 - 3.80: 41 3.80 - 5.06: 8 5.06 - 6.33: 4 Bond angle restraints: 10056 Sorted by residual: angle pdb=" N GLU A 591 " pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " ideal model delta sigma weight residual 110.22 114.61 -4.39 1.54e+00 4.22e-01 8.13e+00 angle pdb=" O3' DG C 2 " pdb=" C3' DG C 2 " pdb=" C2' DG C 2 " ideal model delta sigma weight residual 111.50 108.21 3.29 1.50e+00 4.44e-01 4.82e+00 angle pdb=" CB MET A 25 " pdb=" CG MET A 25 " pdb=" SD MET A 25 " ideal model delta sigma weight residual 112.70 119.03 -6.33 3.00e+00 1.11e-01 4.45e+00 angle pdb=" CB ARG A 41 " pdb=" CG ARG A 41 " pdb=" CD ARG A 41 " ideal model delta sigma weight residual 111.30 116.04 -4.74 2.30e+00 1.89e-01 4.24e+00 angle pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " pdb=" CG GLU A 591 " ideal model delta sigma weight residual 114.10 118.21 -4.11 2.00e+00 2.50e-01 4.22e+00 ... (remaining 10051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 3964 34.02 - 68.03: 241 68.03 - 102.05: 16 102.05 - 136.06: 2 136.06 - 170.08: 2 Dihedral angle restraints: 4225 sinusoidal: 2177 harmonic: 2048 Sorted by residual: dihedral pdb=" O4' U F 3 " pdb=" C1' U F 3 " pdb=" N1 U F 3 " pdb=" C2 U F 3 " ideal model delta sinusoidal sigma weight residual 200.00 29.92 170.08 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U F 44 " pdb=" C1' U F 44 " pdb=" N1 U F 44 " pdb=" C2 U F 44 " ideal model delta sinusoidal sigma weight residual -160.00 -103.50 -56.50 1 1.50e+01 4.44e-03 1.91e+01 dihedral pdb=" C4' DT E 11 " pdb=" C3' DT E 11 " pdb=" O3' DT E 11 " pdb=" P DA E 12 " ideal model delta sinusoidal sigma weight residual 220.00 79.58 140.42 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 4222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 802 0.031 - 0.062: 273 0.062 - 0.092: 64 0.092 - 0.123: 38 0.123 - 0.154: 8 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA GLU A 591 " pdb=" N GLU A 591 " pdb=" C GLU A 591 " pdb=" CB GLU A 591 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA LYS A 625 " pdb=" N LYS A 625 " pdb=" C LYS A 625 " pdb=" CB LYS A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 193 " pdb=" N ILE A 193 " pdb=" C ILE A 193 " pdb=" CB ILE A 193 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.610 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.008 0.661 7145 Z= 0.301 Angle : 0.490 6.331 10056 Z= 0.265 Chirality : 0.037 0.154 1185 Planarity : 0.003 0.032 1014 Dihedral : 19.381 170.081 2901 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 covalent geometry : bond 0.00332 ( 7142) covalent geometry : angle 0.48978 (10056) hydrogen bonds : bond 0.19328 ( 339) hydrogen bonds : angle 6.99053 ( 892) metal coordination : bond 0.38155 ( 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 : 0.160 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: 0.5533 time to fit residues: 43.1851 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 : 0.210 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 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: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.139974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104588 restraints weight = 9553.545| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.16 r_work: 0.3236 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7145 Z= 0.207 Angle : 0.541 7.026 10056 Z= 0.290 Chirality : 0.039 0.151 1185 Planarity : 0.004 0.032 1014 Dihedral : 21.113 171.135 1811 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.96 % Allowed : 6.46 % 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: 1.65 (0.32), residues: 699 helix: 2.31 (0.29), residues: 312 sheet: -0.23 (0.58), residues: 82 loop : 0.29 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 643 TYR 0.024 0.002 TYR A 218 PHE 0.014 0.002 PHE A 488 TRP 0.014 0.001 TRP A 636 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7142) covalent geometry : angle 0.54148 (10056) hydrogen bonds : bond 0.04450 ( 339) hydrogen bonds : angle 4.45065 ( 892) metal coordination : bond 0.00977 ( 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 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 391 ARG cc_start: 0.8499 (ptp-170) cc_final: 0.8245 (ptp-170) REVERT: A 621 ASP cc_start: 0.8148 (t70) cc_final: 0.7441 (t70) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.5679 time to fit residues: 37.9005 Evaluate side-chains 55 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 222 ASN 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 591 GLU Chi-restraints excluded: chain A residue 627 ASN Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 726 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 5 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3836 r_free = 0.3836 target = 0.145111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111104 restraints weight = 9575.035| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.14 r_work: 0.3325 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7145 Z= 0.107 Angle : 0.470 6.331 10056 Z= 0.253 Chirality : 0.037 0.152 1185 Planarity : 0.003 0.030 1014 Dihedral : 20.920 168.958 1811 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.57 % Allowed : 10.37 % Favored : 88.06 % 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: 1.77 (0.32), residues: 699 helix: 2.36 (0.29), residues: 316 sheet: -0.26 (0.58), residues: 82 loop : 0.41 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 483 TYR 0.021 0.001 TYR A 218 PHE 0.016 0.001 PHE A 488 TRP 0.011 0.001 TRP A 636 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7142) covalent geometry : angle 0.47048 (10056) hydrogen bonds : bond 0.03572 ( 339) hydrogen bonds : angle 3.95665 ( 892) metal coordination : bond 0.00227 ( 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 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 621 ASP cc_start: 0.8086 (t70) cc_final: 0.7372 (t70) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.4561 time to fit residues: 30.2378 Evaluate side-chains 53 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 0.0070 chunk 19 optimal weight: 2.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.140972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107119 restraints weight = 9659.240| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.05 r_work: 0.3322 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1588 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= 0.193 Angle : 0.510 6.308 10056 Z= 0.272 Chirality : 0.038 0.135 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.014 171.606 1811 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.13 % Allowed : 10.37 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.32), residues: 699 helix: 2.30 (0.29), residues: 315 sheet: -0.04 (0.62), residues: 74 loop : 0.42 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 492 TYR 0.026 0.002 TYR A 218 PHE 0.013 0.001 PHE A 488 TRP 0.010 0.001 TRP A 636 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7142) covalent geometry : angle 0.51049 (10056) hydrogen bonds : bond 0.03838 ( 339) hydrogen bonds : angle 4.07300 ( 892) metal coordination : bond 0.00185 ( 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 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.239 Fit side-chains REVERT: A 610 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 621 ASP cc_start: 0.8209 (t70) cc_final: 0.7562 (t70) outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.4621 time to fit residues: 31.0516 Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 285 THR 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 610 ILE Chi-restraints excluded: chain A residue 627 ASN Chi-restraints excluded: chain A residue 633 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106623 restraints weight = 9490.032| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.13 r_work: 0.3262 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7145 Z= 0.131 Angle : 0.483 7.369 10056 Z= 0.256 Chirality : 0.037 0.172 1185 Planarity : 0.003 0.030 1014 Dihedral : 20.977 171.060 1811 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.94 % Allowed : 11.74 % Favored : 85.32 % 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: 2.37 (0.29), residues: 315 sheet: -0.47 (0.58), residues: 82 loop : 0.32 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.024 0.001 TYR A 218 PHE 0.010 0.001 PHE A 640 TRP 0.011 0.001 TRP A 636 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7142) covalent geometry : angle 0.48348 (10056) hydrogen bonds : bond 0.03446 ( 339) hydrogen bonds : angle 3.98762 ( 892) metal coordination : bond 0.00114 ( 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 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.234 Fit side-chains REVERT: A 513 MET cc_start: 0.6994 (mmt) cc_final: 0.6789 (mmt) REVERT: A 621 ASP cc_start: 0.8106 (t70) cc_final: 0.7447 (t70) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.4033 time to fit residues: 27.4014 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 : 0.238 ------------------------------------------------------------------------------- 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 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 614 VAL Chi-restraints excluded: chain A residue 627 ASN 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: 0.0010 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3192 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.139900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104072 restraints weight = 9409.483| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.14 r_work: 0.3227 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7145 Z= 0.177 Angle : 0.493 7.146 10056 Z= 0.264 Chirality : 0.038 0.143 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.002 172.477 1811 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.52 % Allowed : 11.55 % Favored : 84.93 % 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: 1.83 (0.32), residues: 699 helix: 2.47 (0.29), residues: 309 sheet: -0.18 (0.62), residues: 74 loop : 0.39 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.030 0.002 TYR A 218 PHE 0.010 0.001 PHE A 640 TRP 0.011 0.001 TRP A 636 HIS 0.003 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7142) covalent geometry : angle 0.49315 (10056) hydrogen bonds : bond 0.03655 ( 339) hydrogen bonds : angle 4.02797 ( 892) metal coordination : bond 0.00122 ( 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 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.153 Fit side-chains REVERT: A 610 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8029 (tp) REVERT: A 621 ASP cc_start: 0.8132 (t70) cc_final: 0.7499 (t70) outliers start: 18 outliers final: 12 residues processed: 64 average time/residue: 0.4395 time to fit residues: 30.1478 Evaluate side-chains 62 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 610 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 627 ASN 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: 1.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104849 restraints weight = 9426.076| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.10 r_work: 0.3217 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7145 Z= 0.172 Angle : 0.496 8.741 10056 Z= 0.263 Chirality : 0.038 0.132 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.016 173.049 1811 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.13 % Allowed : 12.72 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.32), residues: 699 helix: 2.36 (0.29), residues: 315 sheet: -0.23 (0.61), residues: 74 loop : 0.35 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 691 TYR 0.030 0.001 TYR A 218 PHE 0.012 0.001 PHE A 341 TRP 0.011 0.001 TRP A 636 HIS 0.003 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7142) covalent geometry : angle 0.49585 (10056) hydrogen bonds : bond 0.03564 ( 339) hydrogen bonds : angle 4.00967 ( 892) metal coordination : bond 0.00120 ( 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 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.236 Fit side-chains REVERT: A 610 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8034 (tp) REVERT: A 621 ASP cc_start: 0.8100 (t70) cc_final: 0.7413 (t70) outliers start: 16 outliers final: 13 residues processed: 63 average time/residue: 0.4272 time to fit residues: 28.9579 Evaluate side-chains 64 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 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 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 627 ASN 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: 7.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103479 restraints weight = 9503.401| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.13 r_work: 0.3206 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7145 Z= 0.182 Angle : 0.509 7.449 10056 Z= 0.269 Chirality : 0.038 0.133 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.025 174.042 1811 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.13 % Allowed : 12.92 % Favored : 83.95 % 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: 2.36 (0.29), residues: 315 sheet: -0.42 (0.58), residues: 80 loop : 0.39 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.032 0.002 TYR A 218 PHE 0.013 0.001 PHE A 341 TRP 0.012 0.001 TRP A 675 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7142) covalent geometry : angle 0.50939 (10056) hydrogen bonds : bond 0.03642 ( 339) hydrogen bonds : angle 4.04415 ( 892) metal coordination : bond 0.00118 ( 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 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.222 Fit side-chains REVERT: A 610 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 621 ASP cc_start: 0.8110 (t70) cc_final: 0.7475 (t70) outliers start: 16 outliers final: 13 residues processed: 61 average time/residue: 0.4494 time to fit residues: 29.4187 Evaluate side-chains 61 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER 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 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 627 ASN 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: 4.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3759 r_free = 0.3759 target = 0.138772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103038 restraints weight = 9412.980| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.12 r_work: 0.3212 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7145 Z= 0.192 Angle : 0.520 9.495 10056 Z= 0.272 Chirality : 0.038 0.133 1185 Planarity : 0.003 0.031 1014 Dihedral : 21.019 175.171 1811 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.33 % Allowed : 13.31 % 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: 1.71 (0.32), residues: 699 helix: 2.34 (0.29), residues: 315 sheet: -0.43 (0.58), residues: 80 loop : 0.39 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.035 0.002 TYR A 218 PHE 0.011 0.001 PHE A 640 TRP 0.014 0.001 TRP A 675 HIS 0.002 0.000 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 7142) covalent geometry : angle 0.51976 (10056) hydrogen bonds : bond 0.03673 ( 339) hydrogen bonds : angle 4.06352 ( 892) metal coordination : bond 0.00125 ( 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 64 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.223 Fit side-chains REVERT: A 391 ARG cc_start: 0.8603 (ptp-170) cc_final: 0.8395 (ptp-170) REVERT: A 610 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8042 (tp) REVERT: A 621 ASP cc_start: 0.8142 (t70) cc_final: 0.7548 (t70) outliers start: 17 outliers final: 15 residues processed: 61 average time/residue: 0.4770 time to fit residues: 31.0664 Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 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 63 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 285 THR 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 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 627 ASN 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: 3.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104792 restraints weight = 9479.085| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.10 r_work: 0.3231 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7145 Z= 0.137 Angle : 0.500 7.760 10056 Z= 0.264 Chirality : 0.037 0.134 1185 Planarity : 0.003 0.032 1014 Dihedral : 21.007 175.274 1811 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.94 % Allowed : 13.70 % 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: 1.75 (0.32), residues: 699 helix: 2.37 (0.29), residues: 315 sheet: -0.50 (0.57), residues: 78 loop : 0.44 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 492 TYR 0.035 0.001 TYR A 218 PHE 0.011 0.001 PHE A 640 TRP 0.015 0.001 TRP A 675 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7142) covalent geometry : angle 0.49965 (10056) hydrogen bonds : bond 0.03493 ( 339) hydrogen bonds : angle 4.02061 ( 892) metal coordination : bond 0.00108 ( 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 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.226 Fit side-chains REVERT: A 610 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 621 ASP cc_start: 0.8154 (t70) cc_final: 0.7477 (t70) outliers start: 15 outliers final: 13 residues processed: 66 average time/residue: 0.4081 time to fit residues: 29.1437 Evaluate side-chains 62 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 227 LEU 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 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 627 ASN 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: 4.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 478 GLN A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097589 restraints weight = 9545.334| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.21 r_work: 0.3136 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.061 7145 Z= 0.432 Angle : 0.683 8.722 10056 Z= 0.359 Chirality : 0.047 0.163 1185 Planarity : 0.004 0.028 1014 Dihedral : 21.365 175.438 1811 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.13 % Allowed : 13.89 % Favored : 82.97 % 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: 1.29 (0.32), residues: 699 helix: 1.97 (0.29), residues: 317 sheet: -0.68 (0.59), residues: 83 loop : 0.21 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 492 TYR 0.049 0.003 TYR A 218 PHE 0.016 0.002 PHE A 341 TRP 0.019 0.002 TRP A 675 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00979 ( 7142) covalent geometry : angle 0.68261 (10056) hydrogen bonds : bond 0.05110 ( 339) hydrogen bonds : angle 4.46407 ( 892) metal coordination : bond 0.00349 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.72 seconds wall clock time: 49 minutes 47.56 seconds (2987.56 seconds total)