Starting phenix.real_space_refine on Sat Aug 23 03:44:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u53_41911/08_2025/8u53_41911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u53_41911/08_2025/8u53_41911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u53_41911/08_2025/8u53_41911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u53_41911/08_2025/8u53_41911.map" model { file = "/net/cci-nas-00/data/ceres_data/8u53_41911/08_2025/8u53_41911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u53_41911/08_2025/8u53_41911.cif" } resolution = 2.6 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= 0.004 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 34 5.16 5 C 6476 2.51 5 N 1442 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9562 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1439 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "B" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3078 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'UNK:plan-1': 37} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'82T': 1, 'CPL': 1, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 1.64, per 1000 atoms: 0.17 Number of scatterers: 9562 At special positions: 0 Unit cell: (130.81, 118.45, 90.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 4 15.00 O 1606 8.00 N 1442 7.00 C 6476 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: 0.81 Conformation dependent library (CDL) restraints added in 293.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 84.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 Processing helix chain 'A' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY A 32 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 184 Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 281 through 303 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 355 through 377 Processing helix chain 'A' and resid 377 through 388 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 428 through 439 removed outlier: 3.503A pdb=" N LEU A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 464 through 474 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 501 through 523 removed outlier: 3.841A pdb=" N TYR A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 537 Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.591A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 573 Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 578 through 601 Processing helix chain 'A' and resid 612 through 638 Processing helix chain 'A' and resid 642 through 645 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'B' and resid 3 through 28 Processing helix chain 'B' and resid 29 through 32 removed outlier: 6.543A pdb=" N GLY B 32 " --> pdb=" O ARG B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 78 through 102 removed outlier: 3.529A pdb=" N LEU B 101 " --> pdb=" O CYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 184 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 281 through 303 Processing helix chain 'B' and resid 317 through 325 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 355 through 377 Processing helix chain 'B' and resid 377 through 388 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.504A pdb=" N LEU B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 463 Processing helix chain 'B' and resid 464 through 474 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 501 through 523 removed outlier: 3.841A pdb=" N TYR B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 540 through 549 removed outlier: 3.591A pdb=" N TRP B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 573 Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 578 through 601 Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 642 through 645 Processing helix chain 'B' and resid 646 through 665 Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 685 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 229 removed outlier: 3.530A pdb=" N ARG A 226 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 226 through 229 removed outlier: 3.531A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1587 1.31 - 1.44: 3076 1.44 - 1.58: 4940 1.58 - 1.71: 121 1.71 - 1.84: 60 Bond restraints: 9784 Sorted by residual: bond pdb=" O4P CPL A 801 " pdb=" P CPL A 801 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O4P CPL B 802 " pdb=" P CPL B 802 " ideal model delta sigma weight residual 1.648 1.798 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C10 82T B 803 " pdb=" C9 82T B 803 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C10 82T A 802 " pdb=" C9 82T A 802 " ideal model delta sigma weight residual 1.524 1.379 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" CB LEU B 566 " pdb=" CG LEU B 566 " ideal model delta sigma weight residual 1.530 1.397 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 12324 3.28 - 6.56: 773 6.56 - 9.84: 49 9.84 - 13.13: 6 13.13 - 16.41: 4 Bond angle restraints: 13156 Sorted by residual: angle pdb=" N VAL B 601 " pdb=" CA VAL B 601 " pdb=" C VAL B 601 " ideal model delta sigma weight residual 111.62 118.85 -7.23 7.90e-01 1.60e+00 8.38e+01 angle pdb=" N VAL A 601 " pdb=" CA VAL A 601 " pdb=" C VAL A 601 " ideal model delta sigma weight residual 111.62 118.82 -7.20 7.90e-01 1.60e+00 8.31e+01 angle pdb=" C ALA A 576 " pdb=" N PRO A 577 " pdb=" CA PRO A 577 " ideal model delta sigma weight residual 119.56 128.78 -9.22 1.02e+00 9.61e-01 8.17e+01 angle pdb=" C ALA B 576 " pdb=" N PRO B 577 " pdb=" CA PRO B 577 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" CA PHE A 513 " pdb=" CB PHE A 513 " pdb=" CG PHE A 513 " ideal model delta sigma weight residual 113.80 122.41 -8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 13151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 5670 34.85 - 69.70: 120 69.70 - 104.56: 16 104.56 - 139.41: 4 139.41 - 174.26: 6 Dihedral angle restraints: 5816 sinusoidal: 2434 harmonic: 3382 Sorted by residual: dihedral pdb=" C3 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C2 CPL B 802 " pdb=" O3P CPL B 802 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 72.09 -102.17 174.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C2 CPL A 801 " pdb=" O3P CPL A 801 " ideal model delta sinusoidal sigma weight residual 309.18 135.88 173.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1076 0.106 - 0.212: 319 0.212 - 0.318: 61 0.318 - 0.424: 6 0.424 - 0.530: 6 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C2 CPL A 801 " pdb=" C1 CPL A 801 " pdb=" C3 CPL A 801 " pdb=" O2 CPL A 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C2 CPL B 802 " pdb=" C1 CPL B 802 " pdb=" C3 CPL B 802 " pdb=" O2 CPL B 802 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CG LEU A 102 " pdb=" CB LEU A 102 " pdb=" CD1 LEU A 102 " pdb=" CD2 LEU A 102 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 1465 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " -0.068 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR A 171 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 171 " 0.068 2.00e-02 2.50e+03 3.44e-02 2.37e+01 pdb=" CG TYR B 171 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 171 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 171 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 171 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 171 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 171 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 171 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " 0.045 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR B 215 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " 0.048 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4899 2.98 - 3.46: 9897 3.46 - 3.94: 15885 3.94 - 4.42: 20207 4.42 - 4.90: 29622 Nonbonded interactions: 80510 Sorted by model distance: nonbonded pdb=" NH1 ARG A 178 " pdb=" O GLY A 667 " model vdw 2.498 3.120 nonbonded pdb=" NH1 ARG B 178 " pdb=" O GLY B 667 " model vdw 2.499 3.120 nonbonded pdb=" C SER A 501 " pdb=" OG SER A 501 " model vdw 2.534 2.616 nonbonded pdb=" C SER B 501 " pdb=" OG SER B 501 " model vdw 2.534 2.616 nonbonded pdb=" CB PLM A 809 " pdb=" CE PLM A 809 " model vdw 2.553 3.072 ... (remaining 80505 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 697 or resid 804 through 812)) selection = (chain 'B' and (resid 2 through 697 or resid 804 through 812)) } 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: 0.680 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.530 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.024 0.150 9784 Z= 1.271 Angle : 1.715 16.408 13156 Z= 1.115 Chirality : 0.104 0.530 1468 Planarity : 0.009 0.036 1572 Dihedral : 15.246 174.260 3624 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: 0.71 (0.24), residues: 1054 helix: 0.53 (0.17), residues: 742 sheet: None (None), residues: 0 loop : 0.70 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 359 TYR 0.068 0.009 TYR A 171 PHE 0.037 0.007 PHE A 513 TRP 0.045 0.009 TRP A 336 HIS 0.006 0.002 HIS A 696 Details of bonding type rmsd covalent geometry : bond 0.02432 ( 9784) covalent geometry : angle 1.71491 (13156) hydrogen bonds : bond 0.14151 ( 655) hydrogen bonds : angle 6.72633 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7298 (tt0) cc_final: 0.7037 (tt0) REVERT: B 343 GLU cc_start: 0.7362 (tt0) cc_final: 0.7078 (tt0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.4049 time to fit residues: 78.0802 Evaluate side-chains 121 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113953 restraints weight = 14282.433| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.86 r_work: 0.3505 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9784 Z= 0.157 Angle : 0.597 8.703 13156 Z= 0.326 Chirality : 0.042 0.160 1468 Planarity : 0.005 0.042 1572 Dihedral : 17.437 176.710 1666 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.37 % Allowed : 7.10 % Favored : 90.54 % 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 aren not related in a simple way. whole: 1.81 (0.25), residues: 1054 helix: 1.52 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.58 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.018 0.002 TYR B 536 PHE 0.037 0.002 PHE B 513 TRP 0.019 0.002 TRP B 613 HIS 0.004 0.001 HIS A 696 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9784) covalent geometry : angle 0.59742 (13156) hydrogen bonds : bond 0.05096 ( 655) hydrogen bonds : angle 5.19437 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.219 Fit side-chains REVERT: A 428 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.5793 (tmt) REVERT: A 431 LYS cc_start: 0.7131 (tmtt) cc_final: 0.6867 (tttm) REVERT: A 554 SER cc_start: 0.8892 (m) cc_final: 0.8679 (t) REVERT: A 579 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7827 (pp) REVERT: B 554 SER cc_start: 0.8885 (m) cc_final: 0.8667 (t) REVERT: B 579 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7866 (pp) outliers start: 22 outliers final: 7 residues processed: 161 average time/residue: 0.3640 time to fit residues: 63.6053 Evaluate side-chains 122 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.133216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.111390 restraints weight = 14300.721| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.85 r_work: 0.3452 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.183 Angle : 0.598 7.578 13156 Z= 0.320 Chirality : 0.043 0.164 1468 Planarity : 0.005 0.039 1572 Dihedral : 16.696 176.474 1666 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.90 % Allowed : 10.65 % Favored : 86.45 % 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 aren not related in a simple way. whole: 1.59 (0.25), residues: 1054 helix: 1.44 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.22 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 56 TYR 0.015 0.002 TYR A 171 PHE 0.029 0.002 PHE A 513 TRP 0.019 0.002 TRP B 613 HIS 0.005 0.002 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9784) covalent geometry : angle 0.59760 (13156) hydrogen bonds : bond 0.04819 ( 655) hydrogen bonds : angle 5.06333 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.256 Fit side-chains REVERT: A 428 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6026 (tmt) REVERT: A 431 LYS cc_start: 0.7170 (tmtt) cc_final: 0.6886 (tttm) REVERT: A 554 SER cc_start: 0.8892 (m) cc_final: 0.8564 (p) REVERT: A 579 ILE cc_start: 0.8364 (tt) cc_final: 0.7857 (pp) REVERT: B 332 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8575 (mtp) REVERT: B 428 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6026 (tmt) REVERT: B 431 LYS cc_start: 0.7257 (tmtt) cc_final: 0.6986 (tttm) REVERT: B 579 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7855 (pp) outliers start: 27 outliers final: 13 residues processed: 149 average time/residue: 0.3228 time to fit residues: 52.7124 Evaluate side-chains 139 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.135198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.113685 restraints weight = 14463.471| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.85 r_work: 0.3486 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9784 Z= 0.131 Angle : 0.520 6.679 13156 Z= 0.279 Chirality : 0.040 0.152 1468 Planarity : 0.004 0.034 1572 Dihedral : 16.073 173.933 1666 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.26 % Allowed : 12.47 % Favored : 85.27 % 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 aren not related in a simple way. whole: 1.91 (0.25), residues: 1054 helix: 1.66 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.47 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.015 0.001 TYR B 157 PHE 0.027 0.002 PHE A 513 TRP 0.015 0.002 TRP B 613 HIS 0.003 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9784) covalent geometry : angle 0.52015 (13156) hydrogen bonds : bond 0.04211 ( 655) hydrogen bonds : angle 4.86789 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.258 Fit side-chains REVERT: A 76 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 431 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6935 (tttm) REVERT: A 554 SER cc_start: 0.8854 (m) cc_final: 0.8489 (p) REVERT: A 579 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7832 (pp) REVERT: B 76 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8543 (tp) REVERT: B 428 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6015 (tmt) REVERT: B 431 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6949 (tttm) REVERT: B 579 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7807 (pp) outliers start: 21 outliers final: 8 residues processed: 135 average time/residue: 0.3034 time to fit residues: 45.4302 Evaluate side-chains 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112220 restraints weight = 14427.261| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.85 r_work: 0.3466 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9784 Z= 0.146 Angle : 0.532 6.743 13156 Z= 0.283 Chirality : 0.041 0.158 1468 Planarity : 0.004 0.034 1572 Dihedral : 15.889 172.688 1666 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.58 % Allowed : 12.47 % Favored : 84.95 % 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 aren not related in a simple way. whole: 1.72 (0.26), residues: 1054 helix: 1.57 (0.18), residues: 762 sheet: None (None), residues: 0 loop : 0.18 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.010 0.001 TYR A 157 PHE 0.028 0.002 PHE A 513 TRP 0.015 0.002 TRP B 613 HIS 0.004 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9784) covalent geometry : angle 0.53210 (13156) hydrogen bonds : bond 0.04208 ( 655) hydrogen bonds : angle 4.82246 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.378 Fit side-chains REVERT: A 76 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 428 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.5946 (tmt) REVERT: A 431 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6895 (tttm) REVERT: A 554 SER cc_start: 0.8870 (m) cc_final: 0.8483 (p) REVERT: A 579 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7830 (pp) REVERT: B 76 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8512 (tp) REVERT: B 428 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6131 (tmt) REVERT: B 431 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6927 (tttm) REVERT: B 579 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7801 (pp) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 0.4458 time to fit residues: 66.5677 Evaluate side-chains 136 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.0670 chunk 84 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 40.0000 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.115964 restraints weight = 14423.988| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.85 r_work: 0.3519 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9784 Z= 0.112 Angle : 0.488 7.297 13156 Z= 0.258 Chirality : 0.039 0.142 1468 Planarity : 0.004 0.030 1572 Dihedral : 15.445 172.110 1666 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.15 % Allowed : 13.23 % Favored : 84.62 % 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 aren not related in a simple way. whole: 2.07 (0.26), residues: 1054 helix: 1.81 (0.19), residues: 752 sheet: None (None), residues: 0 loop : 0.38 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 56 TYR 0.018 0.001 TYR A 225 PHE 0.024 0.001 PHE B 513 TRP 0.014 0.001 TRP B 548 HIS 0.003 0.001 HIS B 696 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9784) covalent geometry : angle 0.48803 (13156) hydrogen bonds : bond 0.03708 ( 655) hydrogen bonds : angle 4.61946 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.368 Fit side-chains REVERT: A 71 GLN cc_start: 0.8615 (tp40) cc_final: 0.8410 (mm-40) REVERT: A 76 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8447 (tp) REVERT: A 161 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7715 (mm) REVERT: A 222 GLU cc_start: 0.6709 (mp0) cc_final: 0.6450 (tt0) REVERT: A 428 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6051 (tmt) REVERT: A 431 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6885 (tttm) REVERT: A 554 SER cc_start: 0.8801 (m) cc_final: 0.8391 (p) REVERT: A 579 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7702 (pp) REVERT: B 71 GLN cc_start: 0.8580 (tp40) cc_final: 0.8364 (mm-40) REVERT: B 76 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 222 GLU cc_start: 0.6578 (mp0) cc_final: 0.6294 (tt0) REVERT: B 428 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6203 (tmt) REVERT: B 431 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6899 (tttm) REVERT: B 579 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7726 (pp) outliers start: 20 outliers final: 7 residues processed: 132 average time/residue: 0.4697 time to fit residues: 67.7179 Evaluate side-chains 131 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110937 restraints weight = 14464.095| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.88 r_work: 0.3450 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9784 Z= 0.160 Angle : 0.552 8.509 13156 Z= 0.292 Chirality : 0.042 0.161 1468 Planarity : 0.004 0.033 1572 Dihedral : 15.647 170.697 1666 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 13.76 % Favored : 84.09 % 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 aren not related in a simple way. whole: 1.72 (0.26), residues: 1054 helix: 1.61 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.04 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 450 TYR 0.010 0.002 TYR A 157 PHE 0.029 0.002 PHE A 513 TRP 0.016 0.002 TRP B 613 HIS 0.005 0.002 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9784) covalent geometry : angle 0.55238 (13156) hydrogen bonds : bond 0.04203 ( 655) hydrogen bonds : angle 4.72702 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.393 Fit side-chains REVERT: A 76 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 198 ASP cc_start: 0.8652 (m-30) cc_final: 0.8425 (m-30) REVERT: A 222 GLU cc_start: 0.6695 (mp0) cc_final: 0.6371 (tt0) REVERT: A 428 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6035 (tmt) REVERT: A 431 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6893 (tttm) REVERT: A 662 GLN cc_start: 0.8665 (mm110) cc_final: 0.8444 (mm110) REVERT: B 76 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 222 GLU cc_start: 0.6583 (mp0) cc_final: 0.6274 (tt0) REVERT: B 428 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6296 (tmt) REVERT: B 431 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6935 (tttm) outliers start: 20 outliers final: 7 residues processed: 135 average time/residue: 0.4585 time to fit residues: 67.7339 Evaluate side-chains 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.134932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113290 restraints weight = 14462.943| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.86 r_work: 0.3480 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.133 Angle : 0.516 7.655 13156 Z= 0.275 Chirality : 0.040 0.151 1468 Planarity : 0.004 0.032 1572 Dihedral : 15.531 170.332 1666 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.94 % Allowed : 14.52 % Favored : 83.55 % 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 aren not related in a simple way. whole: 1.88 (0.26), residues: 1054 helix: 1.73 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.18 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.019 0.001 TYR B 225 PHE 0.027 0.002 PHE A 513 TRP 0.014 0.002 TRP B 548 HIS 0.004 0.001 HIS A 696 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9784) covalent geometry : angle 0.51596 (13156) hydrogen bonds : bond 0.03937 ( 655) hydrogen bonds : angle 4.64333 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.349 Fit side-chains REVERT: A 76 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8524 (tp) REVERT: A 222 GLU cc_start: 0.6626 (mp0) cc_final: 0.6321 (tt0) REVERT: A 414 GLU cc_start: 0.7810 (pt0) cc_final: 0.7409 (tm-30) REVERT: A 428 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6028 (tmt) REVERT: A 431 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6897 (tttm) REVERT: B 76 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8533 (tp) REVERT: B 222 GLU cc_start: 0.6603 (mp0) cc_final: 0.6309 (tt0) REVERT: B 428 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6269 (tmt) REVERT: B 431 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6916 (tttm) outliers start: 18 outliers final: 6 residues processed: 127 average time/residue: 0.4616 time to fit residues: 63.6645 Evaluate side-chains 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.135294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113765 restraints weight = 14417.172| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.85 r_work: 0.3484 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9784 Z= 0.127 Angle : 0.517 8.196 13156 Z= 0.273 Chirality : 0.040 0.151 1468 Planarity : 0.004 0.032 1572 Dihedral : 15.509 169.678 1666 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.47 % Allowed : 14.30 % Favored : 83.23 % 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 aren not related in a simple way. whole: 1.96 (0.26), residues: 1054 helix: 1.77 (0.19), residues: 752 sheet: None (None), residues: 0 loop : 0.25 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.018 0.001 TYR A 225 PHE 0.026 0.002 PHE B 513 TRP 0.014 0.002 TRP B 613 HIS 0.004 0.001 HIS B 696 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9784) covalent geometry : angle 0.51716 (13156) hydrogen bonds : bond 0.03851 ( 655) hydrogen bonds : angle 4.60836 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.225 Fit side-chains REVERT: A 76 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8520 (tp) REVERT: A 222 GLU cc_start: 0.6608 (mp0) cc_final: 0.6305 (tt0) REVERT: A 414 GLU cc_start: 0.7762 (pt0) cc_final: 0.7364 (tm-30) REVERT: A 428 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6027 (tmt) REVERT: A 431 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6900 (tttm) REVERT: B 76 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8526 (tp) REVERT: B 222 GLU cc_start: 0.6591 (mp0) cc_final: 0.6292 (tt0) REVERT: B 428 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.5992 (tmt) REVERT: B 431 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6947 (tttm) outliers start: 23 outliers final: 9 residues processed: 134 average time/residue: 0.4617 time to fit residues: 67.2386 Evaluate side-chains 133 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 36 optimal weight: 0.0030 chunk 81 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.111826 restraints weight = 14396.663| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.85 r_work: 0.3452 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9784 Z= 0.157 Angle : 0.560 9.096 13156 Z= 0.296 Chirality : 0.042 0.159 1468 Planarity : 0.004 0.033 1572 Dihedral : 15.578 168.649 1666 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.94 % Allowed : 15.05 % Favored : 83.01 % 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 aren not related in a simple way. whole: 1.61 (0.26), residues: 1054 helix: 1.56 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.11 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.018 0.002 TYR B 225 PHE 0.029 0.002 PHE B 513 TRP 0.015 0.002 TRP B 613 HIS 0.005 0.002 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9784) covalent geometry : angle 0.55950 (13156) hydrogen bonds : bond 0.04141 ( 655) hydrogen bonds : angle 4.70918 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.362 Fit side-chains REVERT: A 76 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8554 (tp) REVERT: A 222 GLU cc_start: 0.6612 (mp0) cc_final: 0.6293 (tt0) REVERT: A 414 GLU cc_start: 0.7785 (pt0) cc_final: 0.7330 (tm-30) REVERT: A 428 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.5947 (tmt) REVERT: A 431 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6933 (tttm) REVERT: B 76 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8556 (tp) REVERT: B 222 GLU cc_start: 0.6606 (mp0) cc_final: 0.6284 (tt0) REVERT: B 428 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6038 (tmt) REVERT: B 431 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6933 (tttm) outliers start: 18 outliers final: 8 residues processed: 134 average time/residue: 0.4233 time to fit residues: 61.9770 Evaluate side-chains 137 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.134373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112859 restraints weight = 14301.201| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.84 r_work: 0.3471 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9784 Z= 0.138 Angle : 0.537 9.061 13156 Z= 0.284 Chirality : 0.041 0.152 1468 Planarity : 0.004 0.035 1572 Dihedral : 15.534 168.418 1666 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.94 % Allowed : 15.16 % Favored : 82.90 % 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 aren not related in a simple way. whole: 1.79 (0.26), residues: 1054 helix: 1.68 (0.19), residues: 752 sheet: None (None), residues: 0 loop : 0.08 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.020 0.001 TYR A 225 PHE 0.028 0.002 PHE A 513 TRP 0.014 0.002 TRP B 613 HIS 0.004 0.001 HIS B 696 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9784) covalent geometry : angle 0.53664 (13156) hydrogen bonds : bond 0.03942 ( 655) hydrogen bonds : angle 4.66570 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.32 seconds wall clock time: 55 minutes 55.48 seconds (3355.48 seconds total)