Starting phenix.real_space_refine on Tue Feb 3 21:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ld1_62999/02_2026/9ld1_62999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ld1_62999/02_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_62999/02_2026/9ld1_62999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ld1_62999/02_2026/9ld1_62999_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ld1_62999/02_2026/9ld1_62999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ld1_62999/02_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-2.0-5952/lib/python3.9/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: 1.38, per 1000 atoms: 0.20 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 253.1 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: 0.82 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: 1.07 Time building geometry restraints manager: 0.66 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=" 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=" 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 bond pdb=" N ARG A 380 " pdb=" CA ARG A 380 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.28e-02 6.10e+03 7.20e+00 bond pdb=" N LEU A 381 " pdb=" CA LEU A 381 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 7.02e+00 bond pdb=" N HIS A 820 " pdb=" CA HIS A 820 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.17e-02 7.31e+03 6.56e+00 ... (remaining 7161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 9340 1.33 - 2.67: 545 2.67 - 4.00: 85 4.00 - 5.33: 33 5.33 - 6.67: 8 Bond angle restraints: 10011 Sorted by residual: 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=" C3' DG C 2 " pdb=" O3' DG C 2 " pdb=" P DG C 3 " ideal model delta sigma weight residual 120.20 114.63 5.57 1.50e+00 4.44e-01 1.38e+01 angle pdb=" C3' DA B -9 " pdb=" O3' DA B -9 " pdb=" P DA B -8 " ideal model delta sigma weight residual 120.20 114.98 5.22 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C3' DC B -10 " pdb=" O3' DC B -10 " pdb=" P DA B -9 " ideal model delta sigma weight residual 120.20 115.03 5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" O GLN A 373 " pdb=" C GLN A 373 " pdb=" N ALA A 374 " ideal model delta sigma weight residual 122.03 125.52 -3.49 1.04e+00 9.25e-01 1.12e+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 - 0.106: 1105 0.106 - 0.212: 102 0.212 - 0.318: 0 0.318 - 0.423: 0 0.423 - 0.529: 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 2.35 -2.87 -0.53 2.00e-01 2.50e+01 7.00e+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 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.14e+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 2.35 -2.82 -0.47 2.00e-01 2.50e+01 5.59e+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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.010 Set scattering table: 0.030 Process input model: 8.640 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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= 0.464 Angle : 0.762 6.668 10011 Z= 0.476 Chirality : 0.060 0.529 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 covalent geometry : bond 0.00740 ( 7166) covalent geometry : angle 0.76237 (10011) hydrogen bonds : bond 0.19684 ( 435) hydrogen bonds : angle 9.24346 ( 1259) metal coordination : bond 0.31336 ( 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 : 0.208 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: 0.5593 time to fit residues: 57.2908 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 : 0.181 ------------------------------------------------------------------------------- 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: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 311 GLN A 355 HIS A 447 GLN A 470 HIS A 481 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.238488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.220377 restraints weight = 5636.178| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 0.52 r_work: 0.4049 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7169 Z= 0.162 Angle : 0.569 5.545 10011 Z= 0.311 Chirality : 0.040 0.168 1211 Planarity : 0.005 0.032 1130 Dihedral : 20.765 67.855 1426 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.48 % Allowed : 5.57 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 801 helix: 0.92 (0.21), residues: 549 sheet: 1.14 (0.64), residues: 64 loop : -0.13 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.013 0.001 TYR A 840 PHE 0.014 0.003 PHE A 803 TRP 0.008 0.002 TRP A 772 HIS 0.008 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7166) covalent geometry : angle 0.56876 (10011) hydrogen bonds : bond 0.04197 ( 435) hydrogen bonds : angle 5.53996 ( 1259) metal coordination : bond 0.00644 ( 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: 9 poor density : 56 time to evaluate : 0.232 Fit side-chains REVERT: A 156 GLU cc_start: 0.6326 (mp0) cc_final: 0.6123 (mp0) REVERT: A 165 ASP cc_start: 0.6870 (m-30) cc_final: 0.6579 (m-30) REVERT: A 211 LEU cc_start: 0.7152 (mt) cc_final: 0.6920 (mp) REVERT: A 452 VAL cc_start: 0.7714 (m) cc_final: 0.7499 (p) REVERT: A 698 ARG cc_start: 0.6866 (ttp-170) cc_final: 0.6592 (ttp-110) REVERT: A 816 ARG cc_start: 0.5844 (mtt180) cc_final: 0.5298 (mtp180) REVERT: A 866 THR cc_start: 0.8367 (m) cc_final: 0.7748 (p) outliers start: 9 outliers final: 3 residues processed: 63 average time/residue: 0.5501 time to fit residues: 36.5460 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 : 0.227 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 30 optimal weight: 6.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 243 GLN A 311 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 = 0.4689 r_free = 0.4689 target = 0.250395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.240558 restraints weight = 5508.939| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 0.63 r_work: 0.4223 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7169 Z= 0.167 Angle : 0.565 5.576 10011 Z= 0.308 Chirality : 0.039 0.149 1211 Planarity : 0.004 0.032 1130 Dihedral : 20.795 65.574 1426 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.31 % Allowed : 6.89 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 801 helix: 1.06 (0.22), residues: 548 sheet: 0.99 (0.67), residues: 64 loop : -0.18 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 550 TYR 0.009 0.001 TYR A 840 PHE 0.009 0.002 PHE A 803 TRP 0.010 0.002 TRP A 772 HIS 0.008 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7166) covalent geometry : angle 0.56464 (10011) hydrogen bonds : bond 0.03918 ( 435) hydrogen bonds : angle 5.28095 ( 1259) metal coordination : bond 0.00282 ( 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 58 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.236 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 0.4330 time to fit residues: 25.8958 Evaluate side-chains 41 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 68 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 82 optimal weight: 0.0470 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 219 HIS A 277 GLN A 457 HIS A 491 HIS A 661 HIS A 817 ASN A 818 ASN A 842 ASN A 845 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.252672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.242789 restraints weight = 5410.194| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 0.63 r_work: 0.4278 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3920 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= 0.196 Angle : 0.604 5.657 10011 Z= 0.326 Chirality : 0.040 0.149 1211 Planarity : 0.004 0.033 1130 Dihedral : 20.990 65.029 1426 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.13 % Allowed : 7.54 % Favored : 90.33 % 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: 0.71 (0.28), residues: 801 helix: 0.85 (0.21), residues: 552 sheet: 0.93 (0.67), residues: 62 loop : -0.58 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 550 TYR 0.010 0.001 TYR A 812 PHE 0.012 0.003 PHE A 858 TRP 0.010 0.002 TRP A 772 HIS 0.009 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7166) covalent geometry : angle 0.60403 (10011) hydrogen bonds : bond 0.04006 ( 435) hydrogen bonds : angle 5.30841 ( 1259) metal coordination : bond 0.00205 ( 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 59 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.155 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 54 average time/residue: 0.3767 time to fit residues: 21.9525 Evaluate side-chains 51 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.0030 chunk 82 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4743 r_free = 0.4743 target = 0.255877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.246213 restraints weight = 5512.530| |-----------------------------------------------------------------------------| r_work (start): 0.4660 rms_B_bonded: 0.64 r_work: 0.4318 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.4185 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7169 Z= 0.139 Angle : 0.530 5.578 10011 Z= 0.288 Chirality : 0.038 0.133 1211 Planarity : 0.004 0.034 1130 Dihedral : 20.532 64.892 1426 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.31 % Allowed : 9.84 % 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: 1.05 (0.29), residues: 801 helix: 1.14 (0.22), residues: 553 sheet: 0.92 (0.69), residues: 62 loop : -0.52 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 816 TYR 0.010 0.001 TYR A 840 PHE 0.010 0.002 PHE A 803 TRP 0.011 0.001 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7166) covalent geometry : angle 0.53037 (10011) hydrogen bonds : bond 0.03180 ( 435) hydrogen bonds : angle 4.90662 ( 1259) metal coordination : bond 0.00127 ( 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 58 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.157 Fit side-chains REVERT: A 449 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7471 (mp) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.4669 time to fit residues: 26.7069 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 373 GLN A 817 ASN A 818 ASN A 842 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.255932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.248805 restraints weight = 5535.232| |-----------------------------------------------------------------------------| r_work (start): 0.4678 rms_B_bonded: 0.48 r_work: 0.4378 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7169 Z= 0.136 Angle : 0.527 5.555 10011 Z= 0.286 Chirality : 0.037 0.132 1211 Planarity : 0.004 0.037 1130 Dihedral : 20.503 65.333 1426 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.48 % Allowed : 10.66 % 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: 1.23 (0.29), residues: 801 helix: 1.29 (0.22), residues: 552 sheet: 0.97 (0.71), residues: 61 loop : -0.48 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.009 0.001 TYR A 840 PHE 0.010 0.001 PHE A 803 TRP 0.010 0.001 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7166) covalent geometry : angle 0.52740 (10011) hydrogen bonds : bond 0.03080 ( 435) hydrogen bonds : angle 4.82996 ( 1259) metal coordination : bond 0.00099 ( 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: 9 poor density : 46 time to evaluate : 0.232 Fit side-chains REVERT: A 449 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7432 (mp) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.4512 time to fit residues: 24.6579 Evaluate side-chains 49 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4718 r_free = 0.4718 target = 0.253714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.243625 restraints weight = 5495.478| |-----------------------------------------------------------------------------| r_work (start): 0.4630 rms_B_bonded: 0.66 r_work: 0.4280 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4189 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7169 Z= 0.151 Angle : 0.549 5.814 10011 Z= 0.296 Chirality : 0.038 0.137 1211 Planarity : 0.004 0.037 1130 Dihedral : 20.609 65.602 1426 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 1.15 (0.29), residues: 801 helix: 1.25 (0.22), residues: 553 sheet: 0.99 (0.71), residues: 61 loop : -0.61 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.009 0.001 TYR A 840 PHE 0.007 0.001 PHE A 803 TRP 0.008 0.001 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7166) covalent geometry : angle 0.54881 (10011) hydrogen bonds : bond 0.03255 ( 435) hydrogen bonds : angle 4.91266 ( 1259) metal coordination : bond 0.00123 ( 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 59 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.215 Fit side-chains REVERT: A 449 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7473 (mp) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.4761 time to fit residues: 27.9140 Evaluate side-chains 53 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 0.0050 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 842 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.249319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.237577 restraints weight = 5652.509| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 0.81 r_work: 0.4175 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7169 Z= 0.128 Angle : 0.521 6.745 10011 Z= 0.282 Chirality : 0.037 0.128 1211 Planarity : 0.004 0.037 1130 Dihedral : 20.456 65.764 1426 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.15 % Allowed : 11.97 % 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: 1.40 (0.29), residues: 801 helix: 1.44 (0.22), residues: 552 sheet: 1.09 (0.71), residues: 61 loop : -0.50 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 550 TYR 0.008 0.001 TYR A 840 PHE 0.008 0.001 PHE A 803 TRP 0.009 0.001 TRP A 772 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7166) covalent geometry : angle 0.52058 (10011) hydrogen bonds : bond 0.02888 ( 435) hydrogen bonds : angle 4.73799 ( 1259) metal coordination : bond 0.00084 ( 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 51 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.241 Fit side-chains REVERT: A 698 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6895 (ttm-80) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.4510 time to fit residues: 23.3867 Evaluate side-chains 49 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 392 THR Chi-restraints excluded: chain A residue 656 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 842 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.252799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.242677 restraints weight = 5492.507| |-----------------------------------------------------------------------------| r_work (start): 0.4623 rms_B_bonded: 0.66 r_work: 0.4279 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7169 Z= 0.158 Angle : 0.561 7.276 10011 Z= 0.301 Chirality : 0.038 0.138 1211 Planarity : 0.004 0.038 1130 Dihedral : 20.625 65.842 1426 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.31 % Allowed : 11.64 % 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: 1.20 (0.29), residues: 801 helix: 1.27 (0.21), residues: 553 sheet: 1.07 (0.70), residues: 61 loop : -0.56 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 550 TYR 0.008 0.001 TYR A 840 PHE 0.008 0.001 PHE A 803 TRP 0.007 0.001 TRP A 772 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7166) covalent geometry : angle 0.56061 (10011) hydrogen bonds : bond 0.03295 ( 435) hydrogen bonds : angle 4.92074 ( 1259) metal coordination : bond 0.00157 ( 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 55 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.269 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.3839 time to fit residues: 21.1357 Evaluate side-chains 52 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 504 HIS A 842 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.239018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.231028 restraints weight = 5137.250| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 0.51 r_work: 0.4221 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7169 Z= 0.181 Angle : 0.590 6.708 10011 Z= 0.316 Chirality : 0.039 0.146 1211 Planarity : 0.004 0.036 1130 Dihedral : 20.792 64.888 1426 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.31 % Allowed : 11.97 % 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: 0.96 (0.29), residues: 801 helix: 1.07 (0.21), residues: 554 sheet: 1.00 (0.71), residues: 61 loop : -0.60 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.009 0.001 TYR A 840 PHE 0.009 0.002 PHE A 803 TRP 0.008 0.002 TRP A 96 HIS 0.006 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7166) covalent geometry : angle 0.58962 (10011) hydrogen bonds : bond 0.03641 ( 435) hydrogen bonds : angle 5.14109 ( 1259) metal coordination : bond 0.00195 ( 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: 8 poor density : 48 time to evaluate : 0.180 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.3249 time to fit residues: 18.2526 Evaluate side-chains 51 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 65 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 627 HIS A 841 HIS A 842 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.238412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.230365 restraints weight = 5081.851| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 0.51 r_work: 0.4218 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.4082 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7169 Z= 0.186 Angle : 0.599 7.464 10011 Z= 0.321 Chirality : 0.040 0.148 1211 Planarity : 0.004 0.036 1130 Dihedral : 20.811 64.242 1426 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.31 % Allowed : 12.13 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 801 helix: 1.00 (0.21), residues: 554 sheet: 0.99 (0.71), residues: 61 loop : -0.65 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.009 0.001 TYR A 840 PHE 0.007 0.002 PHE A 803 TRP 0.008 0.002 TRP A 96 HIS 0.005 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7166) covalent geometry : angle 0.59922 (10011) hydrogen bonds : bond 0.03678 ( 435) hydrogen bonds : angle 5.17670 ( 1259) metal coordination : bond 0.00217 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.75 seconds wall clock time: 34 minutes 13.45 seconds (2053.45 seconds total)