Starting phenix.real_space_refine on Thu Jul 2 06:01:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ld1_62999/07_2026/9ld1_62999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ld1_62999/07_2026/9ld1_62999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ld1_62999/07_2026/9ld1_62999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ld1_62999/07_2026/9ld1_62999_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ld1_62999/07_2026/9ld1_62999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ld1_62999/07_2026/9ld1_62999.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 54 5.49 5 S 19 5.16 5 C 4169 2.51 5 N 1264 2.21 5 O 1438 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6945 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 559 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 5837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 5837 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 44, 'TRANS': 758} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6640 SG CYS A 848 24.041 38.951 26.728 1.00 84.59 S ATOM 6662 SG CYS A 851 25.479 37.398 23.215 1.00 82.28 S Time building chain proxies: 1.55, per 1000 atoms: 0.22 Number of scatterers: 6945 At special positions: 0 Unit cell: (78.66, 81.51, 121.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 54 15.00 O 1438 8.00 N 1264 7.00 C 4169 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: 0.64 Conformation dependent library (CDL) restraints added in 309.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 820 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 851 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 848 " 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 1 sheets defined 74.5% alpha, 4.9% beta 13 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 4.545A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.799A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 166 through 184 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 220 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 234 through 254 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 268 through 286 Proline residue: A 281 - end of helix removed outlier: 3.592A pdb=" N GLN A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 322 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.502A pdb=" N ALA A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 388 Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 404 through 422 Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 438 through 456 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 472 through 492 Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 494 through 504 removed outlier: 4.226A pdb=" N HIS A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 525 Proline residue: A 519 - end of helix removed outlier: 3.933A pdb=" N GLN A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 540 through 559 Proline residue: A 553 - end of helix removed outlier: 3.997A pdb=" N GLN A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 574 through 592 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 608 through 628 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 642 through 660 Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 664 through 673 Processing helix chain 'A' and resid 676 through 691 Processing helix chain 'A' and resid 692 through 705 Processing helix chain 'A' and resid 715 through 730 Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.738A pdb=" N LYS A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 820 through 832 Processing helix chain 'A' and resid 850 through 859 removed outlier: 5.610A pdb=" N ALA A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 743 through 745 removed outlier: 5.031A pdb=" N GLN A 800 " --> pdb=" O TYR A 710 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1287 1.33 - 1.45: 1780 1.45 - 1.57: 3972 1.57 - 1.69: 106 1.69 - 1.81: 21 Bond restraints: 7166 Sorted by residual: bond pdb=" C3' DA C 17 " pdb=" C2' DA C 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" N LEU A 382 " pdb=" CA LEU A 382 " ideal model delta sigma weight residual 1.462 1.491 -0.030 9.50e-03 1.11e+04 9.70e+00 bond pdb=" C3' DT B -7 " pdb=" C2' DT B -7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.03e+00 bond pdb=" C3' DC C 19 " pdb=" C2' DC C 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" N VAL A 378 " pdb=" CA VAL A 378 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.19e-02 7.06e+03 7.25e+00 ... (remaining 7161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 9191 1.33 - 2.67: 695 2.67 - 4.00: 84 4.00 - 5.33: 33 5.33 - 6.67: 8 Bond angle restraints: 10011 Sorted by residual: angle pdb=" N3 DT B -11 " pdb=" C4 DT B -11 " pdb=" O4 DT B -11 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N LEU A 375 " pdb=" CA LEU A 375 " pdb=" C LEU A 375 " ideal model delta sigma weight residual 110.97 106.29 4.68 1.09e+00 8.42e-01 1.84e+01 angle pdb=" N3 DT B -14 " pdb=" C4 DT B -14 " pdb=" O4 DT B -14 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT B -17 " pdb=" C4 DT B -17 " pdb=" O4 DT B -17 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 10006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3660 17.52 - 35.04: 219 35.04 - 52.56: 209 52.56 - 70.08: 77 70.08 - 87.60: 5 Dihedral angle restraints: 4170 sinusoidal: 1908 harmonic: 2262 Sorted by residual: dihedral pdb=" CA TRP A 772 " pdb=" C TRP A 772 " pdb=" N LEU A 773 " pdb=" CA LEU A 773 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ALA A 875 " pdb=" C ALA A 875 " pdb=" N ASN A 876 " pdb=" CA ASN A 876 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 dihedral pdb=" N LYS A 372 " pdb=" CA LYS A 372 " pdb=" CB LYS A 372 " pdb=" CG LYS A 372 " ideal model delta sinusoidal sigma weight residual 180.00 121.23 58.77 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1105 0.108 - 0.216: 102 0.216 - 0.324: 0 0.324 - 0.432: 0 0.432 - 0.539: 4 Chirality restraints: 1211 Sorted by residual: chirality pdb=" P DA B -9 " pdb=" OP1 DA B -9 " pdb=" OP2 DA B -9 " pdb=" O5' DA B -9 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" P DG C 2 " pdb=" OP1 DG C 2 " pdb=" OP2 DG C 2 " pdb=" O5' DG C 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" P DT C -1 " pdb=" OP1 DT C -1 " pdb=" OP2 DT C -1 " pdb=" O5' DT C -1 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 1208 not shown) Planarity restraints: 1130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 373 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C GLN A 373 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN A 373 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 374 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 375 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C LEU A 375 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 375 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 376 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C -1 " 0.008 2.00e-02 2.50e+03 7.09e-03 1.26e+00 pdb=" N1 DT C -1 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DT C -1 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT C -1 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT C -1 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DT C -1 " -0.006 2.00e-02 2.50e+03 pdb=" O4 DT C -1 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT C -1 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT C -1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C -1 " -0.000 2.00e-02 2.50e+03 ... (remaining 1127 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 79 2.66 - 3.22: 6591 3.22 - 3.78: 11255 3.78 - 4.34: 16495 4.34 - 4.90: 25357 Nonbonded interactions: 59777 Sorted by model distance: nonbonded pdb=" OD1 ASN A 817 " pdb="ZN ZN A 901 " model vdw 2.097 2.230 nonbonded pdb=" O2 DT B -14 " pdb=" N2 DG C 15 " model vdw 2.247 3.120 nonbonded pdb=" O GLN A 373 " pdb=" OG1 THR A 377 " model vdw 2.418 3.040 nonbonded pdb=" ND2 ASN A 300 " pdb=" O SER A 333 " model vdw 2.466 3.120 nonbonded pdb=" N ASN A 814 " pdb=" OD1 ASN A 814 " model vdw 2.503 3.120 ... (remaining 59772 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: 4.250 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 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 : 0.010 0.374 7169 Z= 0.535 Angle : 0.807 6.668 10011 Z= 0.565 Chirality : 0.063 0.539 1211 Planarity : 0.003 0.024 1130 Dihedral : 18.741 87.598 2720 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.34 % 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: -1.36 (0.25), residues: 801 helix: -1.00 (0.18), residues: 552 sheet: 1.47 (0.62), residues: 62 loop : -0.82 (0.36), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 584 TYR 0.001 0.000 TYR A 734 PHE 0.001 0.000 PHE A 706 TRP 0.001 0.000 TRP A 142 HIS 0.005 0.000 HIS A 820 Details of bonding type rmsd/Z covalent geometry : bond 0.00775 / 0.49 ( 7166) covalent geometry : angle 0.80652 / 0.56 (10011) hydrogen bonds : bond 0.19684 / 21.78 ( 435) hydrogen bonds : angle 9.24346 / 12.30 ( 1259) metal coordination : bond 0.31336 / 19.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.227 Fit side-chains REVERT: A 816 ARG cc_start: 0.5470 (mtt180) cc_final: 0.5214 (mtt90) REVERT: A 866 THR cc_start: 0.8487 (m) cc_final: 0.7781 (p) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.6807 time to fit residues: 69.7832 Evaluate side-chains 54 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS A 311 GLN A 355 HIS A 447 GLN A 470 HIS A 481 GLN A 559 HIS A 577 GLN A 651 GLN A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.242733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.209038 restraints weight = 5644.635| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 0.99 r_work: 0.3930 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7169 Z= 0.170 Angle : 0.654 6.760 10011 Z= 0.358 Chirality : 0.044 0.215 1211 Planarity : 0.005 0.049 1130 Dihedral : 21.178 68.399 1426 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.48 % Allowed : 6.07 % Favored : 92.46 % 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: 0.55 (0.27), residues: 801 helix: 0.62 (0.20), residues: 548 sheet: 1.11 (0.63), residues: 61 loop : -0.31 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.006 0.001 TYR A 840 PHE 0.010 0.002 PHE A 803 TRP 0.010 0.002 TRP A 772 HIS 0.009 0.002 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 7166) covalent geometry : angle 0.65409 / 0.36 (10011) hydrogen bonds : bond 0.04904 / 5.40 ( 435) hydrogen bonds : angle 5.90418 / 7.69 ( 1259) metal coordination : bond 0.00986 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.249 Fit side-chains REVERT: A 156 GLU cc_start: 0.6371 (mp0) cc_final: 0.6008 (pm20) REVERT: A 165 ASP cc_start: 0.6769 (m-30) cc_final: 0.6473 (m-30) REVERT: A 413 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: A 426 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7418 (p) REVERT: A 698 ARG cc_start: 0.6807 (ttp-170) cc_final: 0.6565 (ttp-110) REVERT: A 811 ARG cc_start: 0.6851 (ttp-110) cc_final: 0.6517 (mtp85) REVERT: A 816 ARG cc_start: 0.5768 (mtt180) cc_final: 0.5182 (mtp180) REVERT: A 866 THR cc_start: 0.8374 (m) cc_final: 0.7790 (p) outliers start: 9 outliers final: 2 residues processed: 65 average time/residue: 0.5902 time to fit residues: 40.6558 Evaluate side-chains 53 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 426 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 71 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN A 611 GLN A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.237245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.199710 restraints weight = 5577.669| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 0.92 r_work: 0.3859 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 7169 Z= 0.148 Angle : 0.555 7.973 10011 Z= 0.308 Chirality : 0.040 0.133 1211 Planarity : 0.004 0.035 1130 Dihedral : 21.139 66.080 1426 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.80 % Allowed : 7.54 % Favored : 90.66 % 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: 1.03 (0.28), residues: 801 helix: 1.05 (0.22), residues: 548 sheet: 0.98 (0.65), residues: 62 loop : -0.25 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 618 TYR 0.009 0.001 TYR A 840 PHE 0.016 0.003 PHE A 706 TRP 0.008 0.001 TRP A 772 HIS 0.007 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 7166) covalent geometry : angle 0.55543 / 0.31 (10011) hydrogen bonds : bond 0.04357 / 4.69 ( 435) hydrogen bonds : angle 5.44598 / 7.03 ( 1259) metal coordination : bond 0.01059 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.234 Fit side-chains REVERT: A 165 ASP cc_start: 0.6853 (m-30) cc_final: 0.6552 (m-30) REVERT: A 452 VAL cc_start: 0.7754 (m) cc_final: 0.7549 (p) REVERT: A 698 ARG cc_start: 0.6811 (ttp-170) cc_final: 0.6521 (ttp-110) REVERT: A 816 ARG cc_start: 0.5827 (mtt180) cc_final: 0.5232 (mtp180) REVERT: A 866 THR cc_start: 0.8290 (m) cc_final: 0.7644 (p) outliers start: 11 outliers final: 3 residues processed: 58 average time/residue: 0.5082 time to fit residues: 31.4751 Evaluate side-chains 50 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 243 GLN A 457 HIS ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS A 817 ASN A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.238632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.208671 restraints weight = 5540.252| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 1.07 r_work: 0.3859 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 7169 Z= 0.171 Angle : 0.618 5.779 10011 Z= 0.337 Chirality : 0.042 0.140 1211 Planarity : 0.005 0.040 1130 Dihedral : 21.211 64.237 1426 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.13 % Allowed : 7.21 % Favored : 90.66 % 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: 0.79 (0.28), residues: 801 helix: 0.91 (0.21), residues: 549 sheet: 0.68 (0.68), residues: 64 loop : -0.41 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 811 TYR 0.004 0.001 TYR A 840 PHE 0.012 0.002 PHE A 803 TRP 0.010 0.002 TRP A 772 HIS 0.009 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 7166) covalent geometry : angle 0.61838 / 0.34 (10011) hydrogen bonds : bond 0.04144 / 4.34 ( 435) hydrogen bonds : angle 5.34167 / 6.87 ( 1259) metal coordination : bond 0.00402 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.253 Fit side-chains REVERT: A 156 GLU cc_start: 0.6439 (mp0) cc_final: 0.6200 (mp0) REVERT: A 811 ARG cc_start: 0.7240 (ttp-110) cc_final: 0.7029 (ttp80) REVERT: A 816 ARG cc_start: 0.6089 (mtt180) cc_final: 0.5785 (mtt90) REVERT: A 866 THR cc_start: 0.8282 (m) cc_final: 0.7640 (p) outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 0.4562 time to fit residues: 27.9640 Evaluate side-chains 48 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 703 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.0000 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN A 842 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.240906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.228978 restraints weight = 5604.685| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 0.73 r_work: 0.4078 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7169 Z= 0.121 Angle : 0.525 5.350 10011 Z= 0.292 Chirality : 0.038 0.124 1211 Planarity : 0.004 0.034 1130 Dihedral : 21.129 63.923 1426 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.82 % Allowed : 9.02 % Favored : 90.16 % 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: 1.19 (0.29), residues: 801 helix: 1.23 (0.22), residues: 549 sheet: 0.69 (0.68), residues: 64 loop : -0.30 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.008 0.001 TYR A 840 PHE 0.009 0.002 PHE A 803 TRP 0.010 0.001 TRP A 772 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 7166) covalent geometry : angle 0.52475 / 0.29 (10011) hydrogen bonds : bond 0.03332 / 3.56 ( 435) hydrogen bonds : angle 4.96451 / 6.44 ( 1259) metal coordination : bond 0.00170 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.189 Fit side-chains REVERT: A 811 ARG cc_start: 0.7340 (ttp-110) cc_final: 0.7120 (ttp80) REVERT: A 866 THR cc_start: 0.8256 (m) cc_final: 0.7738 (p) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.4652 time to fit residues: 23.8651 Evaluate side-chains 48 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 818 ASN A 842 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.253098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.243483 restraints weight = 5478.001| |-----------------------------------------------------------------------------| r_work (start): 0.4631 rms_B_bonded: 0.62 r_work: 0.4264 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 7169 Z= 0.153 Angle : 0.571 5.521 10011 Z= 0.314 Chirality : 0.040 0.137 1211 Planarity : 0.004 0.034 1130 Dihedral : 21.189 62.741 1426 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.97 % Allowed : 9.34 % Favored : 88.69 % 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: 0.99 (0.29), residues: 801 helix: 1.11 (0.22), residues: 551 sheet: 0.65 (0.68), residues: 64 loop : -0.47 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.006 0.001 TYR A 840 PHE 0.010 0.002 PHE A 803 TRP 0.009 0.002 TRP A 772 HIS 0.007 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 7166) covalent geometry : angle 0.57136 / 0.31 (10011) hydrogen bonds : bond 0.03741 / 3.94 ( 435) hydrogen bonds : angle 5.06245 / 6.52 ( 1259) metal coordination : bond 0.00194 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.299 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 50 average time/residue: 0.4210 time to fit residues: 22.4656 Evaluate side-chains 47 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 703 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 0.0370 chunk 2 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 491 HIS A 661 HIS A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.254815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.245811 restraints weight = 5445.873| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 0.58 r_work: 0.4309 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.4144 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7169 Z= 0.126 Angle : 0.538 5.434 10011 Z= 0.298 Chirality : 0.038 0.127 1211 Planarity : 0.004 0.033 1130 Dihedral : 21.194 62.837 1426 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.64 % Allowed : 9.51 % Favored : 88.85 % 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: 1.10 (0.29), residues: 801 helix: 1.20 (0.22), residues: 553 sheet: 0.62 (0.69), residues: 64 loop : -0.45 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 550 TYR 0.013 0.001 TYR A 812 PHE 0.008 0.002 PHE A 803 TRP 0.009 0.001 TRP A 772 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 7166) covalent geometry : angle 0.53826 / 0.30 (10011) hydrogen bonds : bond 0.03236 / 3.43 ( 435) hydrogen bonds : angle 4.86614 / 6.31 ( 1259) metal coordination : bond 0.00166 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.211 Fit side-chains REVERT: A 811 ARG cc_start: 0.6873 (ttp80) cc_final: 0.6571 (ttp80) outliers start: 10 outliers final: 5 residues processed: 47 average time/residue: 0.3657 time to fit residues: 18.4680 Evaluate side-chains 46 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 789 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.0070 chunk 73 optimal weight: 7.9990 chunk 12 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 661 HIS A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.257575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.248237 restraints weight = 5484.693| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 0.62 r_work: 0.4334 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7169 Z= 0.125 Angle : 0.530 6.786 10011 Z= 0.294 Chirality : 0.038 0.129 1211 Planarity : 0.004 0.033 1130 Dihedral : 21.109 62.100 1426 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.31 % Allowed : 10.16 % Favored : 88.52 % 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: 1.25 (0.29), residues: 801 helix: 1.31 (0.22), residues: 552 sheet: 0.64 (0.69), residues: 64 loop : -0.36 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.009 0.001 TYR A 812 PHE 0.009 0.002 PHE A 803 TRP 0.013 0.001 TRP A 772 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 7166) covalent geometry : angle 0.53004 / 0.29 (10011) hydrogen bonds : bond 0.03170 / 3.35 ( 435) hydrogen bonds : angle 4.79529 / 6.22 ( 1259) metal coordination : bond 0.00111 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.225 Fit side-chains REVERT: A 811 ARG cc_start: 0.6764 (ttp80) cc_final: 0.6416 (ttp80) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.3795 time to fit residues: 20.1102 Evaluate side-chains 49 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 789 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 661 HIS A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.255522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.245893 restraints weight = 5416.233| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 0.62 r_work: 0.4306 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.4117 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7169 Z= 0.141 Angle : 0.552 6.621 10011 Z= 0.305 Chirality : 0.039 0.143 1211 Planarity : 0.004 0.034 1130 Dihedral : 21.077 61.946 1426 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.98 % Allowed : 10.82 % Favored : 88.20 % 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: 1.16 (0.29), residues: 801 helix: 1.24 (0.22), residues: 552 sheet: 0.66 (0.70), residues: 64 loop : -0.41 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.011 0.001 TYR A 812 PHE 0.009 0.002 PHE A 803 TRP 0.007 0.001 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 7166) covalent geometry : angle 0.55208 / 0.31 (10011) hydrogen bonds : bond 0.03362 / 3.59 ( 435) hydrogen bonds : angle 4.88620 / 6.31 ( 1259) metal coordination : bond 0.00182 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.237 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.4146 time to fit residues: 20.6516 Evaluate side-chains 47 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 789 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 661 HIS A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.255657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.245786 restraints weight = 5477.245| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 0.64 r_work: 0.4305 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7169 Z= 0.132 Angle : 0.542 7.280 10011 Z= 0.300 Chirality : 0.039 0.130 1211 Planarity : 0.004 0.034 1130 Dihedral : 21.060 62.283 1426 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.15 % Allowed : 10.98 % Favored : 87.87 % 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: 1.21 (0.29), residues: 801 helix: 1.27 (0.22), residues: 552 sheet: 0.77 (0.71), residues: 63 loop : -0.41 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 811 TYR 0.008 0.001 TYR A 812 PHE 0.009 0.002 PHE A 803 TRP 0.009 0.001 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7166) covalent geometry : angle 0.54192 / 0.30 (10011) hydrogen bonds : bond 0.03205 / 3.40 ( 435) hydrogen bonds : angle 4.82636 / 6.25 ( 1259) metal coordination : bond 0.00132 / 0.07 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.269 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 47 average time/residue: 0.3507 time to fit residues: 17.8300 Evaluate side-chains 48 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 789 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 HIS A 818 ASN A 842 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.255641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.248434 restraints weight = 5412.033| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 0.48 r_work: 0.4364 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7169 Z= 0.135 Angle : 0.548 7.508 10011 Z= 0.304 Chirality : 0.039 0.131 1211 Planarity : 0.004 0.034 1130 Dihedral : 21.069 62.093 1426 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.31 % Allowed : 10.82 % Favored : 87.87 % 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: 1.20 (0.29), residues: 801 helix: 1.26 (0.22), residues: 552 sheet: 0.78 (0.71), residues: 63 loop : -0.42 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 816 TYR 0.008 0.001 TYR A 812 PHE 0.008 0.002 PHE A 706 TRP 0.007 0.001 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 7166) covalent geometry : angle 0.54782 / 0.30 (10011) hydrogen bonds : bond 0.03244 / 3.44 ( 435) hydrogen bonds : angle 4.83491 / 6.25 ( 1259) metal coordination : bond 0.00134 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.07 seconds wall clock time: 35 minutes 53.00 seconds (2153.00 seconds total)