Starting phenix.real_space_refine on Fri Sep 11 00:15:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.map" model { file = "/net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t6v_10387/09_2026/6t6v_10387.cif" } resolution = 4.5 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= 0.005 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 Ca 1 9.91 5 Fe 2 7.16 5 S 22 5.16 5 C 3881 2.51 5 N 977 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5868 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5781 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5777 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 742, 5777 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 35, 'TRANS': 706} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 5963 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {' CA': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 2 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 2 " occ=0.50 Time building chain proxies: 2.10, per 1000 atoms: 0.36 Number of scatterers: 5868 At special positions: 0 Unit cell: (79.268, 71.967, 105.343, 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) Fe 2 26.01 Ca 1 19.99 S 22 16.00 O 985 8.00 N 977 7.00 C 3881 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 471.8 milliseconds 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 69.4% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.539A pdb=" N PHE A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 30 removed outlier: 3.799A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.533A pdb=" N LEU A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 102 removed outlier: 3.817A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.921A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.007A pdb=" N GLU A 171 " --> pdb=" O HIS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 Processing helix chain 'A' and resid 226 through 253 removed outlier: 3.679A pdb=" N VAL A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 309 Processing helix chain 'A' and resid 323 through 355 removed outlier: 3.551A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 352 - end of helix removed outlier: 3.785A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 removed outlier: 3.745A pdb=" N GLY A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 444 through 461 removed outlier: 4.277A pdb=" N LEU A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.945A pdb=" N PHE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.740A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 560 removed outlier: 4.191A pdb=" N GLU A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 560' Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 601 removed outlier: 3.834A pdb=" N LEU A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.739A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 removed outlier: 4.280A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 637 through 651 removed outlier: 4.090A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 670 through 681 Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.509A pdb=" N ILE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.843A pdb=" N ARG A 703 " --> pdb=" O MET A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 720 through 742 removed outlier: 3.590A pdb=" N ASP A 724 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 5.036A pdb=" N PHE A 49 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 removed outlier: 4.233A pdb=" N ILE A 72 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 75 " --> pdb=" O ILE A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 334 hydrogen bonds defined for protein. 972 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: 0.90 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 2618 1.40 - 1.57: 3403 1.57 - 1.75: 0 1.75 - 1.93: 44 1.93 - 2.10: 6 Bond restraints: 6071 Sorted by residual: bond pdb=" C3B HEM A 802 " pdb=" CAB HEM A 802 " ideal model delta sigma weight residual 1.544 1.473 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C3B HEM A 801 " pdb=" CAB HEM A 801 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C3C HEM A 802 " pdb=" CAC HEM A 802 " ideal model delta sigma weight residual 1.544 1.474 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CA LEU A 521 " pdb=" C LEU A 521 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.30e-02 5.92e+03 9.88e+00 ... (remaining 6066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 7568 2.10 - 4.19: 583 4.19 - 6.29: 125 6.29 - 8.39: 35 8.39 - 10.48: 15 Bond angle restraints: 8326 Sorted by residual: angle pdb=" C VAL A 560 " pdb=" N VAL A 561 " pdb=" CA VAL A 561 " ideal model delta sigma weight residual 120.24 125.28 -5.04 6.30e-01 2.52e+00 6.41e+01 angle pdb=" N GLN A 32 " pdb=" CA GLN A 32 " pdb=" C GLN A 32 " ideal model delta sigma weight residual 113.17 103.47 9.70 1.26e+00 6.30e-01 5.93e+01 angle pdb=" C VAL A 561 " pdb=" CA VAL A 561 " pdb=" CB VAL A 561 " ideal model delta sigma weight residual 114.35 107.17 7.18 1.06e+00 8.90e-01 4.59e+01 angle pdb=" N VAL A 561 " pdb=" CA VAL A 561 " pdb=" C VAL A 561 " ideal model delta sigma weight residual 112.61 122.40 -9.79 1.45e+00 4.76e-01 4.56e+01 angle pdb=" N GLY A 405 " pdb=" CA GLY A 405 " pdb=" C GLY A 405 " ideal model delta sigma weight residual 115.64 124.51 -8.87 1.46e+00 4.69e-01 3.69e+01 ... (remaining 8321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2986 17.44 - 34.87: 282 34.87 - 52.31: 66 52.31 - 69.74: 14 69.74 - 87.18: 10 Dihedral angle restraints: 3358 sinusoidal: 1248 harmonic: 2110 Sorted by residual: dihedral pdb=" C2B HEM A 802 " pdb=" C3B HEM A 802 " pdb=" CAB HEM A 802 " pdb=" CBB HEM A 802 " ideal model delta sinusoidal sigma weight residual 180.00 99.38 80.62 2 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" C2C HEM A 801 " pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " pdb=" CBC HEM A 801 " ideal model delta sinusoidal sigma weight residual 0.00 -61.73 61.73 2 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" C2B HEM A 801 " pdb=" C3B HEM A 801 " pdb=" CAB HEM A 801 " pdb=" CBB HEM A 801 " ideal model delta sinusoidal sigma weight residual 180.00 120.41 59.59 2 1.00e+01 1.00e-02 3.57e+01 ... (remaining 3355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 678 0.077 - 0.154: 156 0.154 - 0.231: 35 0.231 - 0.308: 9 0.308 - 0.386: 5 Chirality restraints: 883 Sorted by residual: chirality pdb=" CB THR A 546 " pdb=" CA THR A 546 " pdb=" OG1 THR A 546 " pdb=" CG2 THR A 546 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA THR A 578 " pdb=" N THR A 578 " pdb=" C THR A 578 " pdb=" CB THR A 578 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB THR A 646 " pdb=" CA THR A 646 " pdb=" OG1 THR A 646 " pdb=" CG2 THR A 646 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 880 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 187 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ARG A 187 " 0.086 2.00e-02 2.50e+03 pdb=" O ARG A 187 " -0.032 2.00e-02 2.50e+03 pdb=" N GLN A 188 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 599 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C TRP A 599 " 0.082 2.00e-02 2.50e+03 pdb=" O TRP A 599 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN A 600 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 286 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C LEU A 286 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU A 286 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE A 287 " 0.027 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 63 2.54 - 3.13: 4456 3.13 - 3.72: 10124 3.72 - 4.31: 12944 4.31 - 4.90: 20611 Nonbonded interactions: 48198 Sorted by model distance: nonbonded pdb=" O GLU A 28 " pdb=" CG GLN A 32 " model vdw 1.944 3.440 nonbonded pdb=" OE1 GLU A 407 " pdb="CA CA A 803 " model vdw 2.047 2.510 nonbonded pdb=" O GLU A 28 " pdb=" CB GLN A 32 " model vdw 2.090 3.440 nonbonded pdb=" NE2 HIS A 331 " pdb="FE HEM A 801 " model vdw 2.125 3.080 nonbonded pdb=" OH TYR A 408 " pdb=" O2A HEM A 802 " model vdw 2.161 3.040 ... (remaining 48193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.340 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.640 Find NCS groups from input model: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.015 0.861 6074 Z= 1.177 Angle : 1.341 10.484 8326 Z= 0.759 Chirality : 0.076 0.386 883 Planarity : 0.009 0.051 1040 Dihedral : 15.460 87.178 2018 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Cbeta Deviations : 0.15 % 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: -4.09 (0.25), residues: 741 helix: -2.59 (0.17), residues: 488 sheet: None (None), residues: 0 loop : -2.60 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 90 TYR 0.026 0.003 TYR A 156 PHE 0.029 0.003 PHE A 493 TRP 0.030 0.003 TRP A 338 HIS 0.020 0.003 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00917 / 0.41 ( 6071) covalent geometry : angle 1.34133 / 0.76 ( 8326) hydrogen bonds : bond 0.16218 / 11.23 ( 334) hydrogen bonds : angle 6.96996 / 5.10 ( 972) Misc. bond : bond 0.51405 / 31.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9256 (m) cc_final: 0.8641 (m) REVERT: A 62 GLN cc_start: 0.9068 (mt0) cc_final: 0.8609 (mt0) REVERT: A 87 TRP cc_start: 0.8792 (t-100) cc_final: 0.7958 (t60) REVERT: A 88 LEU cc_start: 0.9579 (tp) cc_final: 0.9338 (tp) REVERT: A 93 MET cc_start: 0.8691 (mmt) cc_final: 0.8420 (mmp) REVERT: A 101 ARG cc_start: 0.9240 (tpp-160) cc_final: 0.8919 (mmm-85) REVERT: A 119 LEU cc_start: 0.9324 (mm) cc_final: 0.8996 (mp) REVERT: A 138 LYS cc_start: 0.9439 (mmtt) cc_final: 0.9080 (mmtm) REVERT: A 153 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6604 (tm-30) REVERT: A 157 ASP cc_start: 0.8097 (m-30) cc_final: 0.7398 (m-30) REVERT: A 296 GLN cc_start: 0.9451 (tm-30) cc_final: 0.9165 (tm-30) REVERT: A 330 TRP cc_start: 0.9039 (m-10) cc_final: 0.8458 (m-10) REVERT: A 382 PHE cc_start: 0.9401 (m-10) cc_final: 0.9062 (m-80) REVERT: A 404 GLN cc_start: 0.9337 (tt0) cc_final: 0.8928 (tt0) REVERT: A 420 PHE cc_start: 0.8903 (t80) cc_final: 0.8582 (t80) REVERT: A 424 CYS cc_start: 0.9549 (m) cc_final: 0.9315 (m) REVERT: A 468 TYR cc_start: 0.8718 (p90) cc_final: 0.8434 (p90) REVERT: A 481 ARG cc_start: 0.9161 (ttt-90) cc_final: 0.8880 (ptm-80) REVERT: A 493 PHE cc_start: 0.9361 (m-10) cc_final: 0.9143 (m-80) REVERT: A 601 MET cc_start: 0.7937 (ttt) cc_final: 0.7272 (mmm) REVERT: A 621 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 638 TYR cc_start: 0.9152 (m-80) cc_final: 0.8884 (m-10) REVERT: A 665 LYS cc_start: 0.8613 (pttp) cc_final: 0.8015 (pttm) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0661 time to fit residues: 18.2779 Evaluate side-chains 161 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 217 HIS A 333 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.066393 restraints weight = 49564.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.070838 restraints weight = 20935.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.074055 restraints weight = 12485.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076224 restraints weight = 8751.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.077980 restraints weight = 6772.948| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.173 6074 Z= 0.191 Angle : 0.851 18.607 8326 Z= 0.401 Chirality : 0.046 0.189 883 Planarity : 0.005 0.033 1040 Dihedral : 7.078 71.383 821 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -2.26 (0.29), residues: 741 helix: -0.98 (0.21), residues: 499 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 703 TYR 0.018 0.002 TYR A 408 PHE 0.022 0.002 PHE A 727 TRP 0.033 0.002 TRP A 480 HIS 0.008 0.002 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 ( 6071) covalent geometry : angle 0.85120 / 0.40 ( 8326) hydrogen bonds : bond 0.04406 / 3.06 ( 334) hydrogen bonds : angle 4.70622 / 3.41 ( 972) Misc. bond : bond 0.13831 / 7.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9333 (m) cc_final: 0.8958 (m) REVERT: A 62 GLN cc_start: 0.9208 (mt0) cc_final: 0.8603 (mt0) REVERT: A 87 TRP cc_start: 0.9195 (t-100) cc_final: 0.8295 (t60) REVERT: A 93 MET cc_start: 0.8816 (mmt) cc_final: 0.8578 (mmp) REVERT: A 97 ASP cc_start: 0.9387 (t70) cc_final: 0.9184 (t0) REVERT: A 101 ARG cc_start: 0.9240 (tpp-160) cc_final: 0.8920 (mmm-85) REVERT: A 123 LEU cc_start: 0.9085 (mt) cc_final: 0.8865 (mt) REVERT: A 153 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6576 (tm-30) REVERT: A 157 ASP cc_start: 0.7868 (m-30) cc_final: 0.6831 (m-30) REVERT: A 330 TRP cc_start: 0.9130 (m-10) cc_final: 0.8876 (m-10) REVERT: A 371 PHE cc_start: 0.9256 (t80) cc_final: 0.8963 (t80) REVERT: A 408 TYR cc_start: 0.9247 (m-80) cc_final: 0.8408 (m-80) REVERT: A 424 CYS cc_start: 0.9522 (m) cc_final: 0.9239 (m) REVERT: A 481 ARG cc_start: 0.9184 (ttt-90) cc_final: 0.8761 (ttt-90) REVERT: A 601 MET cc_start: 0.7773 (ttt) cc_final: 0.6955 (mmm) REVERT: A 708 MET cc_start: 0.8665 (mtm) cc_final: 0.8378 (mtm) REVERT: A 720 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8370 (ttt90) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0577 time to fit residues: 15.2257 Evaluate side-chains 169 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 27 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 672 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.095995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071483 restraints weight = 21974.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.074792 restraints weight = 13037.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.077162 restraints weight = 9152.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078730 restraints weight = 7053.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079641 restraints weight = 5873.186| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.308 6074 Z= 0.156 Angle : 0.747 7.436 8326 Z= 0.362 Chirality : 0.044 0.185 883 Planarity : 0.005 0.036 1040 Dihedral : 6.955 69.333 821 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -1.47 (0.30), residues: 741 helix: -0.33 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.021 0.002 TYR A 173 PHE 0.044 0.002 PHE A 461 TRP 0.027 0.002 TRP A 480 HIS 0.008 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.15 ( 6071) covalent geometry : angle 0.74708 / 0.36 ( 8326) hydrogen bonds : bond 0.03781 / 2.56 ( 334) hydrogen bonds : angle 4.48384 / 3.23 ( 972) Misc. bond : bond 0.19998 / 10.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9363 (m) cc_final: 0.9159 (p) REVERT: A 62 GLN cc_start: 0.9356 (mt0) cc_final: 0.8674 (mt0) REVERT: A 87 TRP cc_start: 0.9173 (t-100) cc_final: 0.8214 (t60) REVERT: A 93 MET cc_start: 0.8785 (mmt) cc_final: 0.8544 (mmp) REVERT: A 97 ASP cc_start: 0.9392 (t70) cc_final: 0.9178 (t0) REVERT: A 101 ARG cc_start: 0.9297 (tpp-160) cc_final: 0.8986 (mmm-85) REVERT: A 157 ASP cc_start: 0.7804 (m-30) cc_final: 0.7097 (m-30) REVERT: A 408 TYR cc_start: 0.9112 (m-80) cc_final: 0.8560 (m-80) REVERT: A 420 PHE cc_start: 0.8948 (t80) cc_final: 0.8716 (t80) REVERT: A 424 CYS cc_start: 0.9509 (m) cc_final: 0.9224 (m) REVERT: A 477 MET cc_start: 0.8970 (tpp) cc_final: 0.8524 (tpp) REVERT: A 478 GLU cc_start: 0.9455 (tp30) cc_final: 0.9238 (tp30) REVERT: A 481 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8694 (ptm160) REVERT: A 505 PHE cc_start: 0.9419 (m-80) cc_final: 0.9179 (m-80) REVERT: A 515 MET cc_start: 0.8297 (mmt) cc_final: 0.7860 (mmp) REVERT: A 601 MET cc_start: 0.7902 (ttt) cc_final: 0.7015 (tpt) REVERT: A 621 GLN cc_start: 0.7036 (tm-30) cc_final: 0.6498 (tm-30) REVERT: A 638 TYR cc_start: 0.8964 (m-10) cc_final: 0.8689 (m-10) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0586 time to fit residues: 15.3867 Evaluate side-chains 167 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 404 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.070680 restraints weight = 22546.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.073896 restraints weight = 13239.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076253 restraints weight = 9180.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077799 restraints weight = 7071.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078808 restraints weight = 5856.813| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.540 6074 Z= 0.197 Angle : 0.782 10.096 8326 Z= 0.376 Chirality : 0.045 0.188 883 Planarity : 0.004 0.041 1040 Dihedral : 6.887 71.969 821 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.31), residues: 741 helix: 0.01 (0.23), residues: 503 sheet: None (None), residues: 0 loop : -2.12 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.016 0.002 TYR A 156 PHE 0.032 0.002 PHE A 461 TRP 0.027 0.002 TRP A 480 HIS 0.008 0.002 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.19 ( 6071) covalent geometry : angle 0.78248 / 0.38 ( 8326) hydrogen bonds : bond 0.03765 / 2.57 ( 334) hydrogen bonds : angle 4.45645 / 3.21 ( 972) Misc. bond : bond 0.34276 / 17.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9323 (m) cc_final: 0.8859 (m) REVERT: A 62 GLN cc_start: 0.9345 (mt0) cc_final: 0.8633 (mt0) REVERT: A 87 TRP cc_start: 0.9186 (t-100) cc_final: 0.8193 (t60) REVERT: A 93 MET cc_start: 0.8839 (mmt) cc_final: 0.8594 (mmp) REVERT: A 97 ASP cc_start: 0.9370 (t70) cc_final: 0.9143 (t0) REVERT: A 101 ARG cc_start: 0.9275 (tpp-160) cc_final: 0.8991 (mmm-85) REVERT: A 157 ASP cc_start: 0.8071 (m-30) cc_final: 0.7719 (m-30) REVERT: A 190 THR cc_start: 0.9374 (t) cc_final: 0.9000 (t) REVERT: A 408 TYR cc_start: 0.8967 (m-80) cc_final: 0.8423 (m-80) REVERT: A 416 GLN cc_start: 0.9371 (mt0) cc_final: 0.8819 (mt0) REVERT: A 424 CYS cc_start: 0.9476 (m) cc_final: 0.9248 (m) REVERT: A 477 MET cc_start: 0.8897 (tpp) cc_final: 0.8445 (tpp) REVERT: A 478 GLU cc_start: 0.9398 (tp30) cc_final: 0.9132 (tp30) REVERT: A 481 ARG cc_start: 0.9065 (ttt-90) cc_final: 0.8494 (ptm160) REVERT: A 505 PHE cc_start: 0.9386 (m-80) cc_final: 0.9179 (m-80) REVERT: A 515 MET cc_start: 0.8309 (mmt) cc_final: 0.7813 (mmp) REVERT: A 592 CYS cc_start: 0.9149 (m) cc_final: 0.8906 (m) REVERT: A 601 MET cc_start: 0.8079 (ttt) cc_final: 0.7225 (tpt) REVERT: A 659 LEU cc_start: 0.8465 (pp) cc_final: 0.8110 (pp) REVERT: A 683 LEU cc_start: 0.9504 (mm) cc_final: 0.9260 (mm) REVERT: A 737 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8818 (tp40) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0572 time to fit residues: 14.2489 Evaluate side-chains 161 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.065934 restraints weight = 47598.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.070362 restraints weight = 20855.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073378 restraints weight = 12537.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.075668 restraints weight = 8904.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077205 restraints weight = 6890.544| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.564 6074 Z= 0.200 Angle : 0.767 9.591 8326 Z= 0.364 Chirality : 0.045 0.191 883 Planarity : 0.005 0.052 1040 Dihedral : 7.010 76.366 821 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -0.76 (0.31), residues: 741 helix: 0.24 (0.23), residues: 503 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 328 TYR 0.016 0.002 TYR A 156 PHE 0.029 0.002 PHE A 461 TRP 0.019 0.002 TRP A 480 HIS 0.007 0.002 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.19 ( 6071) covalent geometry : angle 0.76654 / 0.36 ( 8326) hydrogen bonds : bond 0.03602 / 2.46 ( 334) hydrogen bonds : angle 4.45116 / 3.19 ( 972) Misc. bond : bond 0.35979 / 18.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9332 (m) cc_final: 0.9132 (p) REVERT: A 62 GLN cc_start: 0.9355 (mt0) cc_final: 0.8753 (mt0) REVERT: A 87 TRP cc_start: 0.9216 (t-100) cc_final: 0.8418 (t60) REVERT: A 93 MET cc_start: 0.8833 (mmt) cc_final: 0.8591 (mmp) REVERT: A 97 ASP cc_start: 0.9361 (t70) cc_final: 0.9137 (t0) REVERT: A 101 ARG cc_start: 0.9299 (tpp-160) cc_final: 0.9024 (mmm-85) REVERT: A 157 ASP cc_start: 0.8112 (m-30) cc_final: 0.7771 (m-30) REVERT: A 190 THR cc_start: 0.9374 (t) cc_final: 0.9028 (t) REVERT: A 295 PHE cc_start: 0.9063 (t80) cc_final: 0.8765 (t80) REVERT: A 404 GLN cc_start: 0.9008 (tt0) cc_final: 0.8784 (tt0) REVERT: A 408 TYR cc_start: 0.8892 (m-80) cc_final: 0.8414 (m-80) REVERT: A 416 GLN cc_start: 0.9479 (mt0) cc_final: 0.8846 (mt0) REVERT: A 424 CYS cc_start: 0.9480 (m) cc_final: 0.9261 (m) REVERT: A 477 MET cc_start: 0.8941 (tpp) cc_final: 0.8501 (tpp) REVERT: A 481 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8570 (ptm160) REVERT: A 515 MET cc_start: 0.8397 (mmt) cc_final: 0.7888 (mmp) REVERT: A 592 CYS cc_start: 0.9192 (m) cc_final: 0.8946 (m) REVERT: A 601 MET cc_start: 0.8065 (ttt) cc_final: 0.7292 (tpt) REVERT: A 612 ASN cc_start: 0.9512 (t0) cc_final: 0.8806 (m-40) REVERT: A 659 LEU cc_start: 0.8588 (pp) cc_final: 0.8328 (pp) REVERT: A 737 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8958 (tp40) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0581 time to fit residues: 14.0761 Evaluate side-chains 158 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.089783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.065892 restraints weight = 38542.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.069759 restraints weight = 18608.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072392 restraints weight = 11590.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074508 restraints weight = 8323.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075610 restraints weight = 6443.221| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.703 6074 Z= 0.294 Angle : 0.914 15.281 8326 Z= 0.421 Chirality : 0.049 0.208 883 Planarity : 0.005 0.059 1040 Dihedral : 7.370 78.679 821 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.82 (0.31), residues: 741 helix: 0.15 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 51 TYR 0.019 0.003 TYR A 78 PHE 0.024 0.002 PHE A 461 TRP 0.024 0.002 TRP A 480 HIS 0.005 0.002 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.29 ( 6071) covalent geometry : angle 0.91440 / 0.42 ( 8326) hydrogen bonds : bond 0.03963 / 2.71 ( 334) hydrogen bonds : angle 4.70661 / 3.35 ( 972) Misc. bond : bond 0.45650 / 23.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9323 (m) cc_final: 0.8924 (m) REVERT: A 62 GLN cc_start: 0.9352 (mt0) cc_final: 0.8766 (mt0) REVERT: A 87 TRP cc_start: 0.9240 (t-100) cc_final: 0.8276 (t60) REVERT: A 88 LEU cc_start: 0.9678 (tp) cc_final: 0.9467 (tp) REVERT: A 93 MET cc_start: 0.8868 (mmt) cc_final: 0.8641 (mmp) REVERT: A 97 ASP cc_start: 0.9301 (t70) cc_final: 0.9074 (t0) REVERT: A 101 ARG cc_start: 0.9230 (tpp-160) cc_final: 0.8979 (mmm-85) REVERT: A 371 PHE cc_start: 0.9224 (t80) cc_final: 0.8928 (t80) REVERT: A 408 TYR cc_start: 0.8826 (m-80) cc_final: 0.8464 (m-80) REVERT: A 416 GLN cc_start: 0.9548 (mt0) cc_final: 0.8995 (mt0) REVERT: A 424 CYS cc_start: 0.9492 (m) cc_final: 0.9250 (m) REVERT: A 477 MET cc_start: 0.8981 (tpp) cc_final: 0.8610 (tpp) REVERT: A 481 ARG cc_start: 0.9149 (ttt-90) cc_final: 0.8921 (ttt-90) REVERT: A 515 MET cc_start: 0.8422 (mmt) cc_final: 0.7944 (mmp) REVERT: A 592 CYS cc_start: 0.9144 (m) cc_final: 0.8943 (m) REVERT: A 601 MET cc_start: 0.8144 (ttt) cc_final: 0.7336 (tpt) REVERT: A 612 ASN cc_start: 0.9527 (t0) cc_final: 0.9234 (m-40) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0547 time to fit residues: 12.8539 Evaluate side-chains 149 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 672 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.071536 restraints weight = 21640.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.074768 restraints weight = 12864.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077107 restraints weight = 8987.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078440 restraints weight = 6918.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079652 restraints weight = 5836.640| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.471 6074 Z= 0.145 Angle : 0.756 7.852 8326 Z= 0.353 Chirality : 0.044 0.193 883 Planarity : 0.004 0.041 1040 Dihedral : 7.006 73.260 821 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.66 (0.31), residues: 741 helix: 0.33 (0.23), residues: 493 sheet: None (None), residues: 0 loop : -1.95 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 51 TYR 0.016 0.002 TYR A 406 PHE 0.029 0.002 PHE A 461 TRP 0.025 0.002 TRP A 338 HIS 0.006 0.002 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 6071) covalent geometry : angle 0.75568 / 0.35 ( 8326) hydrogen bonds : bond 0.03626 / 2.47 ( 334) hydrogen bonds : angle 4.43994 / 3.17 ( 972) Misc. bond : bond 0.29075 / 14.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8897 (mt0) cc_final: 0.8612 (mt0) REVERT: A 87 TRP cc_start: 0.9156 (t-100) cc_final: 0.8370 (t-100) REVERT: A 93 MET cc_start: 0.8744 (mmt) cc_final: 0.8540 (mmp) REVERT: A 97 ASP cc_start: 0.9322 (t70) cc_final: 0.9094 (t0) REVERT: A 101 ARG cc_start: 0.9295 (tpp-160) cc_final: 0.9026 (mmm-85) REVERT: A 190 THR cc_start: 0.9317 (t) cc_final: 0.9036 (t) REVERT: A 326 LEU cc_start: 0.9484 (tp) cc_final: 0.9186 (tp) REVERT: A 408 TYR cc_start: 0.8858 (m-80) cc_final: 0.8451 (m-80) REVERT: A 416 GLN cc_start: 0.9350 (mt0) cc_final: 0.8899 (mt0) REVERT: A 424 CYS cc_start: 0.9469 (m) cc_final: 0.9249 (m) REVERT: A 481 ARG cc_start: 0.8967 (ttt-90) cc_final: 0.8452 (ptm160) REVERT: A 505 PHE cc_start: 0.9260 (m-80) cc_final: 0.9025 (m-80) REVERT: A 515 MET cc_start: 0.8407 (mmt) cc_final: 0.7981 (mmp) REVERT: A 592 CYS cc_start: 0.9123 (m) cc_final: 0.8899 (m) REVERT: A 601 MET cc_start: 0.8056 (ttt) cc_final: 0.7200 (tpt) REVERT: A 612 ASN cc_start: 0.9415 (t0) cc_final: 0.9118 (m-40) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0517 time to fit residues: 13.3942 Evaluate side-chains 155 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.068614 restraints weight = 37547.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072843 restraints weight = 18280.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.075821 restraints weight = 11480.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077852 restraints weight = 8281.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079311 restraints weight = 6537.857| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.439 6074 Z= 0.156 Angle : 0.767 9.366 8326 Z= 0.363 Chirality : 0.044 0.184 883 Planarity : 0.005 0.039 1040 Dihedral : 6.961 75.839 821 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.52 (0.31), residues: 741 helix: 0.40 (0.23), residues: 493 sheet: None (None), residues: 0 loop : -1.79 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 51 TYR 0.016 0.002 TYR A 173 PHE 0.027 0.002 PHE A 461 TRP 0.021 0.002 TRP A 338 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.15 ( 6071) covalent geometry : angle 0.76663 / 0.36 ( 8326) hydrogen bonds : bond 0.03627 / 2.48 ( 334) hydrogen bonds : angle 4.47663 / 3.18 ( 972) Misc. bond : bond 0.27616 / 14.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8875 (mt0) cc_final: 0.8476 (mt0) REVERT: A 87 TRP cc_start: 0.9185 (t-100) cc_final: 0.8430 (t-100) REVERT: A 93 MET cc_start: 0.8815 (mmt) cc_final: 0.8613 (mmp) REVERT: A 97 ASP cc_start: 0.9319 (t70) cc_final: 0.9097 (t0) REVERT: A 101 ARG cc_start: 0.9297 (tpp-160) cc_final: 0.8990 (mmm-85) REVERT: A 157 ASP cc_start: 0.8230 (m-30) cc_final: 0.7851 (m-30) REVERT: A 190 THR cc_start: 0.9326 (t) cc_final: 0.9058 (t) REVERT: A 371 PHE cc_start: 0.9222 (t80) cc_final: 0.8935 (t80) REVERT: A 408 TYR cc_start: 0.8763 (m-80) cc_final: 0.8248 (m-80) REVERT: A 416 GLN cc_start: 0.9376 (mt0) cc_final: 0.8901 (mt0) REVERT: A 424 CYS cc_start: 0.9529 (m) cc_final: 0.9277 (m) REVERT: A 461 PHE cc_start: 0.9277 (m-80) cc_final: 0.8928 (m-80) REVERT: A 515 MET cc_start: 0.8397 (mmt) cc_final: 0.7948 (mmp) REVERT: A 536 PHE cc_start: 0.9512 (m-80) cc_final: 0.9194 (m-80) REVERT: A 601 MET cc_start: 0.8149 (ttt) cc_final: 0.7274 (tpt) REVERT: A 612 ASN cc_start: 0.9393 (t0) cc_final: 0.9120 (m-40) REVERT: A 666 LEU cc_start: 0.8823 (mm) cc_final: 0.8575 (pp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0566 time to fit residues: 14.2026 Evaluate side-chains 160 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 50 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069487 restraints weight = 39673.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073714 restraints weight = 18783.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076758 restraints weight = 11718.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078652 restraints weight = 8441.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080356 restraints weight = 6761.598| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.343 6074 Z= 0.142 Angle : 0.741 8.223 8326 Z= 0.352 Chirality : 0.044 0.195 883 Planarity : 0.004 0.037 1040 Dihedral : 6.842 76.076 821 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.18 % Allowed : 0.36 % Favored : 99.47 % 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: -0.38 (0.32), residues: 741 helix: 0.50 (0.23), residues: 493 sheet: None (None), residues: 0 loop : -1.74 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 51 TYR 0.017 0.002 TYR A 406 PHE 0.025 0.002 PHE A 461 TRP 0.020 0.002 TRP A 338 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 6071) covalent geometry : angle 0.74067 / 0.35 ( 8326) hydrogen bonds : bond 0.03407 / 2.30 ( 334) hydrogen bonds : angle 4.38867 / 3.11 ( 972) Misc. bond : bond 0.21719 / 11.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.9046 (mt0) cc_final: 0.8454 (mt0) REVERT: A 87 TRP cc_start: 0.9159 (t-100) cc_final: 0.8421 (t-100) REVERT: A 93 MET cc_start: 0.8806 (mmt) cc_final: 0.8606 (mmp) REVERT: A 97 ASP cc_start: 0.9314 (t70) cc_final: 0.9091 (t0) REVERT: A 101 ARG cc_start: 0.9282 (tpp-160) cc_final: 0.8972 (mmm-85) REVERT: A 157 ASP cc_start: 0.8223 (m-30) cc_final: 0.7841 (m-30) REVERT: A 190 THR cc_start: 0.9327 (t) cc_final: 0.9106 (t) REVERT: A 404 GLN cc_start: 0.8961 (tt0) cc_final: 0.8398 (tt0) REVERT: A 408 TYR cc_start: 0.8885 (m-80) cc_final: 0.8391 (m-80) REVERT: A 416 GLN cc_start: 0.9473 (mt0) cc_final: 0.8975 (mt0) REVERT: A 424 CYS cc_start: 0.9512 (m) cc_final: 0.9243 (m) REVERT: A 461 PHE cc_start: 0.9314 (m-80) cc_final: 0.8947 (m-80) REVERT: A 515 MET cc_start: 0.8397 (mmt) cc_final: 0.7938 (mmp) REVERT: A 563 LEU cc_start: 0.7258 (mt) cc_final: 0.6978 (mt) REVERT: A 585 ASN cc_start: 0.9342 (m-40) cc_final: 0.9131 (m-40) REVERT: A 601 MET cc_start: 0.8132 (ttt) cc_final: 0.7266 (tpt) REVERT: A 638 TYR cc_start: 0.8799 (m-10) cc_final: 0.8425 (m-10) REVERT: A 666 LEU cc_start: 0.8809 (mm) cc_final: 0.8567 (pp) outliers start: 1 outliers final: 1 residues processed: 178 average time/residue: 0.0521 time to fit residues: 13.4971 Evaluate side-chains 156 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 8.9990 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.070337 restraints weight = 43881.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075010 restraints weight = 19724.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078306 restraints weight = 11927.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080621 restraints weight = 8402.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082017 restraints weight = 6487.898| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.268 6074 Z= 0.134 Angle : 0.749 9.162 8326 Z= 0.355 Chirality : 0.044 0.181 883 Planarity : 0.004 0.041 1040 Dihedral : 6.750 75.763 821 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.41 (0.32), residues: 741 helix: 0.49 (0.24), residues: 490 sheet: None (None), residues: 0 loop : -1.74 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 51 TYR 0.025 0.002 TYR A 362 PHE 0.028 0.002 PHE A 461 TRP 0.021 0.002 TRP A 195 HIS 0.005 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 6071) covalent geometry : angle 0.74944 / 0.36 ( 8326) hydrogen bonds : bond 0.03423 / 2.30 ( 334) hydrogen bonds : angle 4.37531 / 3.11 ( 972) Misc. bond : bond 0.16472 / 8.35 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8910 (mt0) cc_final: 0.8404 (mt0) REVERT: A 87 TRP cc_start: 0.9155 (t-100) cc_final: 0.8707 (t-100) REVERT: A 97 ASP cc_start: 0.9326 (t70) cc_final: 0.9099 (t0) REVERT: A 101 ARG cc_start: 0.9276 (tpp-160) cc_final: 0.8962 (mmm-85) REVERT: A 157 ASP cc_start: 0.8241 (m-30) cc_final: 0.7853 (m-30) REVERT: A 285 TYR cc_start: 0.7995 (m-10) cc_final: 0.7746 (m-80) REVERT: A 371 PHE cc_start: 0.9167 (t80) cc_final: 0.8941 (t80) REVERT: A 404 GLN cc_start: 0.8906 (tt0) cc_final: 0.8407 (tt0) REVERT: A 408 TYR cc_start: 0.8800 (m-80) cc_final: 0.8407 (m-80) REVERT: A 416 GLN cc_start: 0.9487 (mt0) cc_final: 0.9000 (mt0) REVERT: A 424 CYS cc_start: 0.9507 (m) cc_final: 0.9242 (m) REVERT: A 461 PHE cc_start: 0.9316 (m-80) cc_final: 0.8919 (m-80) REVERT: A 515 MET cc_start: 0.8384 (mmt) cc_final: 0.7921 (mmp) REVERT: A 563 LEU cc_start: 0.7109 (mt) cc_final: 0.6778 (mt) REVERT: A 585 ASN cc_start: 0.9335 (m-40) cc_final: 0.9132 (m-40) REVERT: A 601 MET cc_start: 0.8136 (ttt) cc_final: 0.7279 (tpt) REVERT: A 666 LEU cc_start: 0.8863 (mm) cc_final: 0.8633 (pp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0525 time to fit residues: 13.6112 Evaluate side-chains 157 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 0.0670 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073274 restraints weight = 25607.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076869 restraints weight = 14181.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079460 restraints weight = 9487.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081340 restraints weight = 7121.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082653 restraints weight = 5707.366| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 6074 Z= 0.142 Angle : 0.748 8.101 8326 Z= 0.355 Chirality : 0.044 0.178 883 Planarity : 0.004 0.045 1040 Dihedral : 6.726 76.457 821 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.42 (0.32), residues: 741 helix: 0.47 (0.24), residues: 499 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.028 0.002 TYR A 406 PHE 0.026 0.002 PHE A 461 TRP 0.021 0.002 TRP A 195 HIS 0.004 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 ( 6071) covalent geometry : angle 0.74812 / 0.36 ( 8326) hydrogen bonds : bond 0.03368 / 2.27 ( 334) hydrogen bonds : angle 4.35191 / 3.10 ( 972) Misc. bond : bond 0.18648 / 9.52 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1101.26 seconds wall clock time: 19 minutes 43.86 seconds (1183.86 seconds total)