Starting phenix.real_space_refine on Tue Aug 4 22:09:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ld1_62999/08_2026/9ld1_62999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ld1_62999/08_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_62999/08_2026/9ld1_62999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ld1_62999/08_2026/9ld1_62999_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ld1_62999/08_2026/9ld1_62999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ld1_62999/08_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-2.2rc3-6140/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: 1.06, per 1000 atoms: 0.15 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: 0.51 Conformation dependent library (CDL) restraints added in 224.4 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: 0.71 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: 0.94 Time building geometry restraints manager: 0.69 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: 85 4.00 - 5.33: 33 5.33 - 6.67: 7 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=" C3' DG C 2 " pdb=" O3' DG C 2 " pdb=" P DG C 3 " ideal model delta sigma weight residual 119.70 114.63 5.07 1.20e+00 6.94e-01 1.79e+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 ... (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: 4.130 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.060 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:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- 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 : 0.806 6.668 10011 Z= 0.567 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 0.80632 / 0.57 (10011) hydrogen bonds : bond 0.19684 / 21.86 ( 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 : 0.161 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: 0.5449 time to fit residues: 55.8776 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 : 0.160 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.243192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.4293 r_free = 0.4293 target = 0.204911 restraints weight = 5643.436| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 0.97 r_work: 0.3952 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1998 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= 0.170 Angle : 0.630 6.172 10011 Z= 0.348 Chirality : 0.043 0.188 1211 Planarity : 0.005 0.043 1130 Dihedral : 21.118 67.285 1426 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.31 % Allowed : 5.90 % Favored : 92.79 % 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: 0.58 (0.27), residues: 801 helix: 0.64 (0.20), residues: 554 sheet: 1.18 (0.63), residues: 61 loop : -0.36 (0.37), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.005 0.001 TYR A 815 PHE 0.010 0.002 PHE A 803 TRP 0.009 0.002 TRP A 772 HIS 0.008 0.002 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 7166) covalent geometry : angle 0.63012 / 0.35 (10011) hydrogen bonds : bond 0.05173 / 5.69 ( 435) hydrogen bonds : angle 5.99186 / 7.82 ( 1259) metal coordination : bond 0.01369 / 0.97 ( 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 65 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.260 Fit side-chains REVERT: A 156 GLU cc_start: 0.6299 (mp0) cc_final: 0.6006 (pm20) REVERT: A 165 ASP cc_start: 0.6718 (m-30) cc_final: 0.6418 (m-30) REVERT: A 426 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7347 (p) REVERT: A 698 ARG cc_start: 0.6793 (ttp-170) cc_final: 0.6547 (ttp-110) REVERT: A 816 ARG cc_start: 0.5769 (mtt180) cc_final: 0.5128 (mtp180) REVERT: A 866 THR cc_start: 0.8397 (m) cc_final: 0.7760 (p) outliers start: 8 outliers final: 2 residues processed: 64 average time/residue: 0.4023 time to fit residues: 27.4018 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 : 0.182 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 40.0000 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 HIS A 559 HIS A 611 GLN 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 = 0.4506 r_free = 0.4506 target = 0.232233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.208442 restraints weight = 5574.662| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 0.66 r_work: 0.3891 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 7169 Z= 0.187 Angle : 0.634 5.590 10011 Z= 0.346 Chirality : 0.044 0.148 1211 Planarity : 0.005 0.035 1130 Dihedral : 21.266 65.727 1426 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.30 % Allowed : 7.05 % 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: 0.61 (0.28), residues: 801 helix: 0.71 (0.21), residues: 549 sheet: 0.90 (0.64), residues: 62 loop : -0.37 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 482 TYR 0.011 0.001 TYR A 840 PHE 0.019 0.004 PHE A 706 TRP 0.009 0.002 TRP A 772 HIS 0.009 0.002 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 ( 7166) covalent geometry : angle 0.63428 / 0.35 (10011) hydrogen bonds : bond 0.04833 / 5.17 ( 435) hydrogen bonds : angle 5.64749 / 7.22 ( 1259) metal coordination : bond 0.01546 / 0.78 ( 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 68 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.162 Fit side-chains REVERT: A 313 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7354 (mt) REVERT: A 452 VAL cc_start: 0.7741 (m) cc_final: 0.7512 (p) REVERT: A 811 ARG cc_start: 0.7180 (ttp-110) cc_final: 0.6828 (mtp85) REVERT: A 816 ARG cc_start: 0.6037 (mtt180) cc_final: 0.5450 (mtp180) REVERT: A 866 THR cc_start: 0.8341 (m) cc_final: 0.7731 (p) outliers start: 14 outliers final: 4 residues processed: 65 average time/residue: 0.3977 time to fit residues: 27.4459 Evaluate side-chains 54 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 813 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 233 ASN A 457 HIS A 627 HIS A 817 ASN A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.251309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.242264 restraints weight = 5369.401| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 0.57 r_work: 0.4286 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 7169 Z= 0.227 Angle : 0.705 6.952 10011 Z= 0.379 Chirality : 0.045 0.162 1211 Planarity : 0.005 0.035 1130 Dihedral : 21.462 64.470 1426 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.62 % Allowed : 7.70 % Favored : 89.67 % 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: 0.17 (0.27), residues: 801 helix: 0.48 (0.21), residues: 552 sheet: 0.45 (0.67), residues: 64 loop : -0.78 (0.37), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 312 TYR 0.005 0.001 TYR A 850 PHE 0.014 0.003 PHE A 706 TRP 0.010 0.002 TRP A 772 HIS 0.009 0.002 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 ( 7166) covalent geometry : angle 0.70484 / 0.38 (10011) hydrogen bonds : bond 0.04821 / 5.10 ( 435) hydrogen bonds : angle 5.63858 / 7.23 ( 1259) metal coordination : bond 0.00430 / 0.25 ( 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 61 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.168 Fit side-chains REVERT: A 129 LYS cc_start: 0.8355 (tptt) cc_final: 0.8117 (tttm) REVERT: A 279 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6827 (mp) REVERT: A 706 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6746 (p90) REVERT: A 866 THR cc_start: 0.8163 (m) cc_final: 0.7910 (p) outliers start: 16 outliers final: 6 residues processed: 58 average time/residue: 0.4297 time to fit residues: 26.5299 Evaluate side-chains 50 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 813 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 277 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 = 0.4734 r_free = 0.4734 target = 0.254840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.245901 restraints weight = 5436.912| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 0.58 r_work: 0.4324 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.4247 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7169 Z= 0.139 Angle : 0.569 5.436 10011 Z= 0.313 Chirality : 0.039 0.127 1211 Planarity : 0.004 0.033 1130 Dihedral : 21.301 64.133 1426 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.48 % Allowed : 10.82 % Favored : 87.70 % 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: 0.69 (0.29), residues: 801 helix: 0.88 (0.22), residues: 553 sheet: 0.48 (0.68), residues: 64 loop : -0.61 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 816 TYR 0.015 0.001 TYR A 812 PHE 0.009 0.002 PHE A 803 TRP 0.011 0.002 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 7166) covalent geometry : angle 0.56913 / 0.31 (10011) hydrogen bonds : bond 0.03653 / 3.91 ( 435) hydrogen bonds : angle 5.14564 / 6.63 ( 1259) metal coordination : bond 0.00192 / 0.10 ( 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 54 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.166 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 51 average time/residue: 0.4049 time to fit residues: 22.0573 Evaluate side-chains 46 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 34 optimal weight: 0.0070 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 277 GLN A 491 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 = 0.4723 r_free = 0.4723 target = 0.253482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.243496 restraints weight = 5450.444| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 0.63 r_work: 0.4292 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7169 Z= 0.156 Angle : 0.587 5.521 10011 Z= 0.320 Chirality : 0.040 0.142 1211 Planarity : 0.004 0.036 1130 Dihedral : 21.202 62.460 1426 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.97 % Allowed : 10.00 % Favored : 88.03 % 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: 0.72 (0.29), residues: 801 helix: 0.93 (0.22), residues: 553 sheet: 0.46 (0.68), residues: 64 loop : -0.65 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.010 0.001 TYR A 812 PHE 0.009 0.002 PHE A 803 TRP 0.011 0.002 TRP A 772 HIS 0.006 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 7166) covalent geometry : angle 0.58664 / 0.32 (10011) hydrogen bonds : bond 0.03808 / 4.05 ( 435) hydrogen bonds : angle 5.17378 / 6.67 ( 1259) metal coordination : bond 0.00189 / 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 55 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.145 Fit side-chains REVERT: A 449 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7426 (mp) outliers start: 12 outliers final: 5 residues processed: 52 average time/residue: 0.3533 time to fit residues: 19.8661 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 : 0.235 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 813 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 0.0570 chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN A 219 HIS A 277 GLN A 504 HIS A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.252920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.242840 restraints weight = 5435.169| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 0.66 r_work: 0.4288 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3978 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= 0.160 Angle : 0.597 6.490 10011 Z= 0.326 Chirality : 0.040 0.148 1211 Planarity : 0.004 0.034 1130 Dihedral : 21.200 61.738 1426 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.80 % Allowed : 10.00 % 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: 0.69 (0.29), residues: 801 helix: 0.92 (0.21), residues: 553 sheet: 0.43 (0.69), residues: 64 loop : -0.70 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.010 0.001 TYR A 812 PHE 0.010 0.002 PHE A 803 TRP 0.009 0.002 TRP A 772 HIS 0.006 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 7166) covalent geometry : angle 0.59708 / 0.33 (10011) hydrogen bonds : bond 0.03741 / 3.98 ( 435) hydrogen bonds : angle 5.14780 / 6.64 ( 1259) metal coordination : bond 0.00244 / 0.12 ( 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 57 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.238 Fit side-chains REVERT: A 449 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7495 (mp) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 0.3446 time to fit residues: 19.6568 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 : 0.134 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 813 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.0050 chunk 73 optimal weight: 0.0970 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.255710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.246433 restraints weight = 5518.419| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 0.64 r_work: 0.4334 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7169 Z= 0.125 Angle : 0.551 7.022 10011 Z= 0.305 Chirality : 0.038 0.132 1211 Planarity : 0.004 0.035 1130 Dihedral : 21.119 61.926 1426 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.48 % Allowed : 11.48 % Favored : 87.05 % 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: 1.04 (0.29), residues: 801 helix: 1.22 (0.22), residues: 552 sheet: 0.26 (0.70), residues: 64 loop : -0.57 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 811 TYR 0.008 0.001 TYR A 840 PHE 0.012 0.002 PHE A 803 TRP 0.010 0.001 TRP A 772 HIS 0.002 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 7166) covalent geometry : angle 0.55106 / 0.31 (10011) hydrogen bonds : bond 0.03199 / 3.43 ( 435) hydrogen bonds : angle 4.90461 / 6.37 ( 1259) metal coordination : bond 0.00065 / 0.03 ( 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 53 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.202 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.3458 time to fit residues: 18.2614 Evaluate side-chains 50 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 813 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 0.0070 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN 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 = 0.4715 r_free = 0.4715 target = 0.252224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.242941 restraints weight = 5422.327| |-----------------------------------------------------------------------------| r_work (start): 0.4630 rms_B_bonded: 0.63 r_work: 0.4293 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7169 Z= 0.169 Angle : 0.607 7.250 10011 Z= 0.330 Chirality : 0.041 0.144 1211 Planarity : 0.004 0.035 1130 Dihedral : 21.180 61.021 1426 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.97 % Allowed : 11.31 % Favored : 86.72 % 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: 0.83 (0.29), residues: 801 helix: 1.03 (0.22), residues: 553 sheet: 0.34 (0.71), residues: 63 loop : -0.63 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.007 0.001 TYR A 840 PHE 0.009 0.002 PHE A 803 TRP 0.007 0.002 TRP A 772 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 7166) covalent geometry : angle 0.60736 / 0.33 (10011) hydrogen bonds : bond 0.03797 / 4.05 ( 435) hydrogen bonds : angle 5.13788 / 6.60 ( 1259) metal coordination : bond 0.00233 / 0.12 ( 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 58 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.181 Fit side-chains REVERT: A 449 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7365 (mp) outliers start: 12 outliers final: 7 residues processed: 53 average time/residue: 0.3643 time to fit residues: 20.7852 Evaluate side-chains 55 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 449 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 813 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 701 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 = 0.4731 r_free = 0.4731 target = 0.254436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.245227 restraints weight = 5488.138| |-----------------------------------------------------------------------------| r_work (start): 0.4654 rms_B_bonded: 0.60 r_work: 0.4321 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.4138 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7169 Z= 0.131 Angle : 0.558 7.531 10011 Z= 0.307 Chirality : 0.039 0.135 1211 Planarity : 0.004 0.034 1130 Dihedral : 21.110 62.140 1426 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.15 % Allowed : 11.80 % Favored : 87.05 % 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: 1.04 (0.29), residues: 801 helix: 1.22 (0.22), residues: 553 sheet: 0.32 (0.71), residues: 63 loop : -0.58 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 811 TYR 0.013 0.001 TYR A 812 PHE 0.009 0.002 PHE A 803 TRP 0.009 0.001 TRP A 772 HIS 0.003 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 7166) covalent geometry : angle 0.55750 / 0.31 (10011) hydrogen bonds : bond 0.03212 / 3.44 ( 435) hydrogen bonds : angle 4.93131 / 6.39 ( 1259) metal coordination : bond 0.00116 / 0.06 ( 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 56 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.224 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.3774 time to fit residues: 21.5828 Evaluate side-chains 54 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 656 VAL 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: 5.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 818 ASN ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.253868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.244711 restraints weight = 5419.982| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 0.63 r_work: 0.4303 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4202 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= 0.141 Angle : 0.571 8.191 10011 Z= 0.314 Chirality : 0.039 0.136 1211 Planarity : 0.004 0.035 1130 Dihedral : 21.079 61.412 1426 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.31 % Allowed : 11.80 % Favored : 86.89 % 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: 1.01 (0.29), residues: 801 helix: 1.19 (0.22), residues: 553 sheet: 0.36 (0.71), residues: 63 loop : -0.60 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 811 TYR 0.014 0.001 TYR A 812 PHE 0.008 0.002 PHE A 803 TRP 0.008 0.001 TRP A 772 HIS 0.003 0.001 HIS A 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 7166) covalent geometry : angle 0.57098 / 0.31 (10011) hydrogen bonds : bond 0.03366 / 3.59 ( 435) hydrogen bonds : angle 4.96011 / 6.41 ( 1259) metal coordination : bond 0.00139 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.99 seconds wall clock time: 30 minutes 46.58 seconds (1846.58 seconds total)