Starting phenix.real_space_refine on Tue Feb 3 22:17:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcy_62996/02_2026/9lcy_62996_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcy_62996/02_2026/9lcy_62996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lcy_62996/02_2026/9lcy_62996_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcy_62996/02_2026/9lcy_62996_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcy_62996/02_2026/9lcy_62996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcy_62996/02_2026/9lcy_62996.map" } resolution = 3.02 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= 0.001 sd= 0.151 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 56 5.49 5 S 21 5.16 5 C 4390 2.51 5 N 1323 2.21 5 O 1503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 7294 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6145 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 46, 'TRANS': 788} Chain: "B" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 570 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 578 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} 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 5828 SG CYS A 842 46.810 55.673 98.034 1.00 29.23 S ATOM 5850 SG CYS A 845 46.032 53.180 100.303 1.00 29.25 S Time building chain proxies: 1.43, per 1000 atoms: 0.20 Number of scatterers: 7294 At special positions: 0 Unit cell: (85.1067, 85.1067, 128.199, 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 21 16.00 P 56 15.00 O 1503 8.00 N 1323 7.00 C 4390 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: 0.61 Conformation dependent library (CDL) restraints added in 231.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 814 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 842 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 845 " 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 1 sheets defined 73.8% alpha, 3.4% beta 24 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 63 through 81 removed outlier: 6.900A pdb=" N GLN A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 4.811A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.715A pdb=" N THR A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 166 through 184 removed outlier: 3.505A pdb=" N ALA A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 217 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 234 through 252 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 268 through 286 removed outlier: 3.682A pdb=" N ALA A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 320 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 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 removed outlier: 3.522A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) 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 491 Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 494 through 504 removed outlier: 4.408A pdb=" N HIS A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 540 through 558 Proline residue: A 553 - end of helix 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 627 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 690 Processing helix chain 'A' and resid 692 through 702 Processing helix chain 'A' and resid 715 through 734 Processing helix chain 'A' and resid 737 through 752 removed outlier: 3.834A pdb=" N ASP A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 842 through 853 removed outlier: 3.528A pdb=" N THR A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 768 removed outlier: 4.434A pdb=" N ALA A 708 " --> pdb=" O GLY A 796 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1777 1.33 - 1.45: 1503 1.45 - 1.57: 4112 1.57 - 1.69: 110 1.69 - 1.81: 25 Bond restraints: 7527 Sorted by residual: bond pdb=" N HIS A 661 " pdb=" CA HIS A 661 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.12e+00 bond pdb=" N THR A 664 " pdb=" CA THR A 664 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.87e+00 bond pdb=" N LEU A 663 " pdb=" CA LEU A 663 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.26e-02 6.30e+03 4.21e+00 bond pdb=" N GLY A 662 " pdb=" CA GLY A 662 " ideal model delta sigma weight residual 1.450 1.478 -0.027 1.41e-02 5.03e+03 3.80e+00 bond pdb=" C GLN A 718 " pdb=" N ILE A 719 " ideal model delta sigma weight residual 1.334 1.311 0.023 1.26e-02 6.30e+03 3.34e+00 ... (remaining 7522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 10248 1.45 - 2.91: 204 2.91 - 4.36: 25 4.36 - 5.81: 20 5.81 - 7.26: 1 Bond angle restraints: 10498 Sorted by residual: angle pdb=" CA LYS A 717 " pdb=" C LYS A 717 " pdb=" N GLN A 718 " ideal model delta sigma weight residual 117.30 113.30 4.00 1.16e+00 7.43e-01 1.19e+01 angle pdb=" O LYS A 717 " pdb=" C LYS A 717 " pdb=" N GLN A 718 " ideal model delta sigma weight residual 122.12 125.66 -3.54 1.06e+00 8.90e-01 1.12e+01 angle pdb=" CA LEU A 663 " pdb=" C LEU A 663 " pdb=" O LEU A 663 " ideal model delta sigma weight residual 120.92 118.12 2.80 1.04e+00 9.25e-01 7.25e+00 angle pdb=" CA GLN A 718 " pdb=" C GLN A 718 " pdb=" O GLN A 718 " ideal model delta sigma weight residual 119.97 116.90 3.07 1.15e+00 7.56e-01 7.14e+00 angle pdb=" C GLN A 718 " pdb=" N ILE A 719 " pdb=" CA ILE A 719 " ideal model delta sigma weight residual 120.42 124.15 -3.73 1.42e+00 4.96e-01 6.91e+00 ... (remaining 10493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 3635 16.75 - 33.51: 462 33.51 - 50.26: 204 50.26 - 67.01: 86 67.01 - 83.76: 9 Dihedral angle restraints: 4396 sinusoidal: 2040 harmonic: 2356 Sorted by residual: dihedral pdb=" CA LEU A 700 " pdb=" C LEU A 700 " pdb=" N MET A 701 " pdb=" CA MET A 701 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG A 550 " pdb=" C ARG A 550 " pdb=" N LEU A 551 " pdb=" CA LEU A 551 " ideal model delta harmonic sigma weight residual 180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ARG A 618 " pdb=" C ARG A 618 " pdb=" N LEU A 619 " pdb=" CA LEU A 619 " ideal model delta harmonic sigma weight residual -180.00 -164.25 -15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 4393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 856 0.032 - 0.065: 285 0.065 - 0.097: 105 0.097 - 0.129: 18 0.129 - 0.161: 3 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA GLN A 718 " pdb=" N GLN A 718 " pdb=" C GLN A 718 " pdb=" CB GLN A 718 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA LEU A 663 " pdb=" N LEU A 663 " pdb=" C LEU A 663 " pdb=" CB LEU A 663 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CG LEU A 700 " pdb=" CB LEU A 700 " pdb=" CD1 LEU A 700 " pdb=" CD2 LEU A 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1264 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 717 " -0.009 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C LYS A 717 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS A 717 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN A 718 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 760 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 761 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 761 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 761 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 562 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 563 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " -0.023 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1043 2.76 - 3.29: 6733 3.29 - 3.83: 12432 3.83 - 4.36: 14915 4.36 - 4.90: 25040 Nonbonded interactions: 60163 Sorted by model distance: nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.224 3.040 nonbonded pdb=" O VAL A 227 " pdb=" OG SER A 231 " model vdw 2.272 3.040 nonbonded pdb=" O VAL A 397 " pdb=" OG SER A 401 " model vdw 2.280 3.040 nonbonded pdb=" O VAL A 601 " pdb=" OG SER A 605 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 809 " pdb=" OP1 DC B 2 " model vdw 2.325 3.040 ... (remaining 60158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.620 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.003 0.034 7530 Z= 0.152 Angle : 0.523 7.264 10498 Z= 0.290 Chirality : 0.038 0.161 1267 Planarity : 0.005 0.043 1178 Dihedral : 19.105 83.762 2884 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.86 (0.29), residues: 833 helix: 1.05 (0.21), residues: 586 sheet: 0.13 (0.75), residues: 49 loop : -0.55 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 100 TYR 0.007 0.001 TYR A 834 PHE 0.002 0.000 PHE A 797 TRP 0.002 0.000 TRP A 96 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7527) covalent geometry : angle 0.52327 (10498) hydrogen bonds : bond 0.14465 ( 463) hydrogen bonds : angle 6.10574 ( 1323) metal coordination : bond 0.00173 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0683 time to fit residues: 7.0997 Evaluate side-chains 53 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 617 GLN A 661 HIS A 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.199768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176405 restraints weight = 6296.895| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 0.64 r_work: 0.3551 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.141 Angle : 0.527 7.621 10498 Z= 0.284 Chirality : 0.038 0.130 1267 Planarity : 0.005 0.047 1178 Dihedral : 20.956 85.648 1476 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.61 % Allowed : 5.17 % Favored : 94.22 % 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 (0.29), residues: 833 helix: 1.22 (0.21), residues: 594 sheet: 0.15 (0.76), residues: 49 loop : -0.57 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 810 TYR 0.006 0.001 TYR A 834 PHE 0.002 0.000 PHE A 797 TRP 0.002 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7527) covalent geometry : angle 0.52714 (10498) hydrogen bonds : bond 0.03089 ( 463) hydrogen bonds : angle 4.25221 ( 1323) metal coordination : bond 0.00216 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.221 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.0748 time to fit residues: 6.3255 Evaluate side-chains 51 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 745 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 82 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.0020 overall best weight: 0.5966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 HIS A 720 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.196799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.180353 restraints weight = 6355.340| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 0.74 r_work: 0.3528 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.133 Angle : 0.504 7.833 10498 Z= 0.270 Chirality : 0.038 0.118 1267 Planarity : 0.005 0.045 1178 Dihedral : 20.778 84.766 1476 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.61 % Allowed : 7.75 % Favored : 91.64 % 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: 1.26 (0.29), residues: 833 helix: 1.38 (0.22), residues: 591 sheet: 0.21 (0.76), residues: 49 loop : -0.54 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 618 TYR 0.006 0.001 TYR A 697 PHE 0.002 0.000 PHE A 797 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7527) covalent geometry : angle 0.50440 (10498) hydrogen bonds : bond 0.02926 ( 463) hydrogen bonds : angle 4.07846 ( 1323) metal coordination : bond 0.00205 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.177 Fit side-chains REVERT: A 702 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7683 (mmm160) REVERT: A 806 TYR cc_start: 0.8620 (m-80) cc_final: 0.8308 (m-80) REVERT: A 810 ARG cc_start: 0.8222 (mtt180) cc_final: 0.8003 (mtt180) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.0922 time to fit residues: 7.1812 Evaluate side-chains 48 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 745 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.192695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.179533 restraints weight = 6423.538| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 0.64 r_work: 0.3562 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7530 Z= 0.197 Angle : 0.568 8.572 10498 Z= 0.302 Chirality : 0.040 0.121 1267 Planarity : 0.005 0.047 1178 Dihedral : 21.155 86.106 1476 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.61 % Allowed : 9.73 % 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: 0.98 (0.29), residues: 833 helix: 1.19 (0.21), residues: 593 sheet: -0.04 (0.71), residues: 52 loop : -0.68 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.007 0.001 TYR A 697 PHE 0.003 0.001 PHE A 852 TRP 0.004 0.001 TRP A 773 HIS 0.003 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 7527) covalent geometry : angle 0.56784 (10498) hydrogen bonds : bond 0.03651 ( 463) hydrogen bonds : angle 4.21280 ( 1323) metal coordination : bond 0.00379 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.194 Fit side-chains REVERT: A 530 GLU cc_start: 0.7484 (mp0) cc_final: 0.7239 (mp0) REVERT: A 701 MET cc_start: 0.8835 (mmm) cc_final: 0.8517 (mmm) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0815 time to fit residues: 5.6830 Evaluate side-chains 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.194405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.181870 restraints weight = 6357.525| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 0.58 r_work: 0.3609 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7530 Z= 0.153 Angle : 0.526 8.900 10498 Z= 0.281 Chirality : 0.038 0.132 1267 Planarity : 0.005 0.048 1178 Dihedral : 20.988 84.700 1476 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.76 % Allowed : 10.79 % Favored : 88.45 % 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: 1.11 (0.29), residues: 833 helix: 1.27 (0.21), residues: 591 sheet: 0.13 (0.75), residues: 49 loop : -0.60 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.013 0.001 TYR A 877 PHE 0.002 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7527) covalent geometry : angle 0.52557 (10498) hydrogen bonds : bond 0.03122 ( 463) hydrogen bonds : angle 4.10738 ( 1323) metal coordination : bond 0.00252 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 810 ARG cc_start: 0.8246 (mtt180) cc_final: 0.8038 (mtt180) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.0898 time to fit residues: 6.4838 Evaluate side-chains 47 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.195368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.180878 restraints weight = 6397.099| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.63 r_work: 0.3576 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.139 Angle : 0.513 9.230 10498 Z= 0.274 Chirality : 0.038 0.116 1267 Planarity : 0.005 0.048 1178 Dihedral : 20.860 84.861 1476 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.06 % Allowed : 10.94 % Favored : 87.99 % 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: 1.27 (0.29), residues: 833 helix: 1.38 (0.22), residues: 591 sheet: 0.28 (0.76), residues: 49 loop : -0.53 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 810 TYR 0.011 0.001 TYR A 877 PHE 0.002 0.000 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7527) covalent geometry : angle 0.51340 (10498) hydrogen bonds : bond 0.02910 ( 463) hydrogen bonds : angle 4.01808 ( 1323) metal coordination : bond 0.00212 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.148 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.0689 time to fit residues: 5.2391 Evaluate side-chains 53 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.193567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.181319 restraints weight = 6341.015| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 0.57 r_work: 0.3600 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7530 Z= 0.175 Angle : 0.546 9.565 10498 Z= 0.290 Chirality : 0.039 0.119 1267 Planarity : 0.005 0.049 1178 Dihedral : 21.037 83.804 1476 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.52 % Allowed : 10.94 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 833 helix: 1.24 (0.21), residues: 593 sheet: 0.23 (0.76), residues: 49 loop : -0.57 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 810 TYR 0.009 0.001 TYR A 877 PHE 0.002 0.001 PHE A 797 TRP 0.004 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7527) covalent geometry : angle 0.54610 (10498) hydrogen bonds : bond 0.03343 ( 463) hydrogen bonds : angle 4.10917 ( 1323) metal coordination : bond 0.00317 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 877 TYR cc_start: 0.8832 (p90) cc_final: 0.8596 (p90) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.0781 time to fit residues: 6.2813 Evaluate side-chains 52 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.196067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.183225 restraints weight = 6400.580| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 0.58 r_work: 0.3616 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.130 Angle : 0.509 9.728 10498 Z= 0.271 Chirality : 0.038 0.130 1267 Planarity : 0.005 0.049 1178 Dihedral : 20.845 82.847 1476 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.91 % Allowed : 11.85 % Favored : 87.23 % 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: 1.31 (0.30), residues: 833 helix: 1.41 (0.22), residues: 591 sheet: 0.35 (0.78), residues: 49 loop : -0.51 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 710 TYR 0.010 0.001 TYR A 877 PHE 0.002 0.000 PHE A 852 TRP 0.003 0.001 TRP A 96 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7527) covalent geometry : angle 0.50897 (10498) hydrogen bonds : bond 0.02773 ( 463) hydrogen bonds : angle 3.98730 ( 1323) metal coordination : bond 0.00174 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.192 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.0754 time to fit residues: 5.7675 Evaluate side-chains 59 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 0.0670 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.195368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.183581 restraints weight = 6340.648| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 0.56 r_work: 0.3630 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.140 Angle : 0.518 9.872 10498 Z= 0.275 Chirality : 0.038 0.119 1267 Planarity : 0.005 0.049 1178 Dihedral : 20.871 82.629 1476 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.37 % Allowed : 11.40 % Favored : 87.23 % 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: 1.37 (0.30), residues: 833 helix: 1.43 (0.22), residues: 591 sheet: 0.34 (0.78), residues: 49 loop : -0.38 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 810 TYR 0.012 0.001 TYR A 877 PHE 0.002 0.000 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7527) covalent geometry : angle 0.51822 (10498) hydrogen bonds : bond 0.02905 ( 463) hydrogen bonds : angle 3.98807 ( 1323) metal coordination : bond 0.00222 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.186 Fit side-chains REVERT: A 530 GLU cc_start: 0.7459 (mp0) cc_final: 0.7229 (mp0) outliers start: 9 outliers final: 9 residues processed: 58 average time/residue: 0.0729 time to fit residues: 5.9068 Evaluate side-chains 56 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 53 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.196829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.183781 restraints weight = 6342.435| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 0.60 r_work: 0.3621 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7530 Z= 0.127 Angle : 0.508 9.991 10498 Z= 0.270 Chirality : 0.038 0.131 1267 Planarity : 0.005 0.048 1178 Dihedral : 20.793 82.599 1476 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.37 % Allowed : 11.40 % Favored : 87.23 % 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: 1.43 (0.30), residues: 833 helix: 1.47 (0.22), residues: 591 sheet: 0.40 (0.78), residues: 49 loop : -0.35 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 810 TYR 0.012 0.001 TYR A 877 PHE 0.002 0.000 PHE A 852 TRP 0.002 0.001 TRP A 96 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7527) covalent geometry : angle 0.50796 (10498) hydrogen bonds : bond 0.02688 ( 463) hydrogen bonds : angle 3.93811 ( 1323) metal coordination : bond 0.00162 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.186 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.0622 time to fit residues: 4.9865 Evaluate side-chains 61 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 875 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.195050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.183005 restraints weight = 6366.332| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 0.56 r_work: 0.3609 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7530 Z= 0.152 Angle : 0.529 10.026 10498 Z= 0.280 Chirality : 0.038 0.122 1267 Planarity : 0.005 0.049 1178 Dihedral : 20.892 83.360 1476 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.37 % Allowed : 11.55 % Favored : 87.08 % 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: 1.35 (0.30), residues: 833 helix: 1.41 (0.22), residues: 591 sheet: 0.37 (0.78), residues: 49 loop : -0.39 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 810 TYR 0.012 0.001 TYR A 877 PHE 0.002 0.000 PHE A 797 TRP 0.003 0.001 TRP A 773 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7527) covalent geometry : angle 0.52924 (10498) hydrogen bonds : bond 0.03022 ( 463) hydrogen bonds : angle 4.00383 ( 1323) metal coordination : bond 0.00266 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.47 seconds wall clock time: 29 minutes 41.20 seconds (1781.20 seconds total)