Starting phenix.real_space_refine on Fri Aug 22 16:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0b_36759/08_2025/8k0b_36759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0b_36759/08_2025/8k0b_36759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k0b_36759/08_2025/8k0b_36759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0b_36759/08_2025/8k0b_36759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k0b_36759/08_2025/8k0b_36759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0b_36759/08_2025/8k0b_36759.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3758 2.51 5 N 945 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5689 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5689 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 25, 'TRANS': 663} Time building chain proxies: 1.49, per 1000 atoms: 0.26 Number of scatterers: 5689 At special positions: 0 Unit cell: (104.94, 93.28, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 952 8.00 N 945 7.00 C 3758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 300 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 223.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 64.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 35 through 61 Processing helix chain 'A' and resid 63 through 73 removed outlier: 4.353A pdb=" N ALA A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.619A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 removed outlier: 3.959A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 146 removed outlier: 3.653A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 140 " --> pdb=" O HIS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 182 through 206 Processing helix chain 'A' and resid 231 through 243 removed outlier: 4.030A pdb=" N ILE A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 285 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.944A pdb=" N ARG A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 334 removed outlier: 4.135A pdb=" N GLN A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.725A pdb=" N VAL A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 406 through 429 Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 446 through 477 removed outlier: 4.132A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Proline residue: A 454 - end of helix Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 480 through 502 removed outlier: 3.968A pdb=" N TYR A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 540 through 560 removed outlier: 4.238A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 3.833A pdb=" N CYS A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.777A pdb=" N VAL A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 617 through 640 removed outlier: 3.938A pdb=" N PHE A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 661 removed outlier: 3.950A pdb=" N HIS A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 677 removed outlier: 3.856A pdb=" N GLY A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.696A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 255 removed outlier: 5.716A pdb=" N LEU A 340 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 223 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A 382 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 318 hydrogen bonds defined for protein. 939 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: 0.83 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 832 1.31 - 1.44: 1783 1.44 - 1.56: 3192 1.56 - 1.69: 0 1.69 - 1.82: 51 Bond restraints: 5858 Sorted by residual: bond pdb=" C TYR A 130 " pdb=" O TYR A 130 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.32e+01 bond pdb=" CA TYR A 130 " pdb=" C TYR A 130 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" CA SER A 687 " pdb=" CB SER A 687 " ideal model delta sigma weight residual 1.530 1.478 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" N TYR A 54 " pdb=" CA TYR A 54 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.82e+00 bond pdb=" N SER A 689 " pdb=" CA SER A 689 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.10e+00 ... (remaining 5853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 7860 3.25 - 6.51: 82 6.51 - 9.76: 14 9.76 - 13.01: 3 13.01 - 16.27: 2 Bond angle restraints: 7961 Sorted by residual: angle pdb=" C TYR A 130 " pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " ideal model delta sigma weight residual 110.96 94.69 16.27 1.54e+00 4.22e-01 1.12e+02 angle pdb=" N HIS A 136 " pdb=" CA HIS A 136 " pdb=" C HIS A 136 " ideal model delta sigma weight residual 112.87 102.31 10.56 1.20e+00 6.94e-01 7.74e+01 angle pdb=" N SER A 687 " pdb=" CA SER A 687 " pdb=" C SER A 687 " ideal model delta sigma weight residual 111.11 101.72 9.39 1.20e+00 6.94e-01 6.12e+01 angle pdb=" C ILE A 131 " pdb=" N THR A 132 " pdb=" CA THR A 132 " ideal model delta sigma weight residual 120.79 111.26 9.53 1.39e+00 5.18e-01 4.70e+01 angle pdb=" C HIS A 136 " pdb=" CA HIS A 136 " pdb=" CB HIS A 136 " ideal model delta sigma weight residual 110.21 124.85 -14.64 2.19e+00 2.09e-01 4.47e+01 ... (remaining 7956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2883 17.46 - 34.91: 389 34.91 - 52.37: 104 52.37 - 69.83: 22 69.83 - 87.29: 9 Dihedral angle restraints: 3407 sinusoidal: 1361 harmonic: 2046 Sorted by residual: dihedral pdb=" C TYR A 130 " pdb=" N TYR A 130 " pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " ideal model delta harmonic sigma weight residual -122.60 -103.89 -18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" CA LEU A 536 " pdb=" C LEU A 536 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " ideal model delta harmonic sigma weight residual 180.00 147.47 32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 300 " pdb=" CB CYS A 300 " ideal model delta sinusoidal sigma weight residual 93.00 145.30 -52.30 1 1.00e+01 1.00e-02 3.73e+01 ... (remaining 3404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 737 0.057 - 0.114: 139 0.114 - 0.171: 11 0.171 - 0.228: 7 0.228 - 0.286: 2 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA TYR A 130 " pdb=" N TYR A 130 " pdb=" C TYR A 130 " pdb=" CB TYR A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA HIS A 136 " pdb=" N HIS A 136 " pdb=" C HIS A 136 " pdb=" CB HIS A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA GLN A 134 " pdb=" N GLN A 134 " pdb=" C GLN A 134 " pdb=" CB GLN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 893 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 128 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ARG A 128 " -0.068 2.00e-02 2.50e+03 pdb=" O ARG A 128 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 129 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 671 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C PHE A 671 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE A 671 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 672 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 193 " -0.031 2.00e-02 2.50e+03 2.11e-02 8.87e+00 pdb=" CG TYR A 193 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 193 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 193 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 193 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 193 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 193 " -0.005 2.00e-02 2.50e+03 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 439 2.74 - 3.28: 5992 3.28 - 3.82: 9520 3.82 - 4.36: 10716 4.36 - 4.90: 17742 Nonbonded interactions: 44409 Sorted by model distance: nonbonded pdb=" OD1 ASN A 636 " pdb=" OG SER A 640 " model vdw 2.195 3.040 nonbonded pdb=" O ASP A 520 " pdb=" NH1 ARG A 530 " model vdw 2.281 3.120 nonbonded pdb=" O PHE A 420 " pdb=" OG1 THR A 424 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP A 339 " pdb=" NH2 ARG A 400 " model vdw 2.325 3.120 nonbonded pdb=" OG1 THR A 278 " pdb=" OE2 GLU A 312 " model vdw 2.338 3.040 ... (remaining 44404 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=1.00 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 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 : 0.004 0.055 5859 Z= 0.230 Angle : 0.865 16.268 7963 Z= 0.506 Chirality : 0.047 0.286 896 Planarity : 0.005 0.057 974 Dihedral : 17.336 87.286 2080 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.28 % Allowed : 31.31 % Favored : 67.41 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.33), residues: 687 helix: 0.59 (0.27), residues: 398 sheet: 0.92 (1.28), residues: 17 loop : -2.07 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.049 0.002 TYR A 193 PHE 0.022 0.001 PHE A 519 TRP 0.017 0.001 TRP A 479 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5858) covalent geometry : angle 0.86471 ( 7961) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.39721 ( 2) hydrogen bonds : bond 0.14938 ( 318) hydrogen bonds : angle 6.52307 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 131 ILE cc_start: 0.6800 (tt) cc_final: 0.6531 (tp) REVERT: A 221 MET cc_start: 0.4513 (tmm) cc_final: 0.3930 (ppp) REVERT: A 671 PHE cc_start: 0.7396 (t80) cc_final: 0.7137 (t80) REVERT: A 688 MET cc_start: 0.6435 (tpp) cc_final: 0.6142 (tpp) outliers start: 8 outliers final: 2 residues processed: 108 average time/residue: 0.0672 time to fit residues: 9.6732 Evaluate side-chains 106 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 691 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.0030 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 197 ASN A 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.240565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.206770 restraints weight = 11028.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.210772 restraints weight = 5655.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.213155 restraints weight = 3655.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.213907 restraints weight = 2825.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.213907 restraints weight = 2539.520| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5859 Z= 0.163 Angle : 0.674 13.028 7963 Z= 0.351 Chirality : 0.043 0.170 896 Planarity : 0.005 0.060 974 Dihedral : 5.466 55.366 766 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.87 % Allowed : 26.36 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.33), residues: 687 helix: 0.72 (0.27), residues: 405 sheet: 0.95 (1.30), residues: 17 loop : -2.05 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.043 0.002 TYR A 193 PHE 0.022 0.001 PHE A 140 TRP 0.018 0.001 TRP A 668 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5858) covalent geometry : angle 0.67441 ( 7961) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.44897 ( 2) hydrogen bonds : bond 0.04714 ( 318) hydrogen bonds : angle 5.16304 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.8034 (t80) cc_final: 0.7514 (t80) REVERT: A 221 MET cc_start: 0.4748 (tmm) cc_final: 0.4314 (ppp) REVERT: A 411 ILE cc_start: 0.7290 (tp) cc_final: 0.7051 (mt) REVERT: A 437 VAL cc_start: -0.2369 (OUTLIER) cc_final: -0.3155 (m) REVERT: A 522 TYR cc_start: 0.1277 (OUTLIER) cc_final: -0.0448 (m-80) REVERT: A 646 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.3748 (pp) REVERT: A 671 PHE cc_start: 0.7289 (t80) cc_final: 0.6707 (t80) outliers start: 43 outliers final: 27 residues processed: 139 average time/residue: 0.0627 time to fit residues: 11.9293 Evaluate side-chains 131 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.0870 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.241447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.207278 restraints weight = 10918.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.211140 restraints weight = 5563.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.213681 restraints weight = 3610.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.215067 restraints weight = 2821.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.215350 restraints weight = 2478.781| |-----------------------------------------------------------------------------| r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5299 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5859 Z= 0.130 Angle : 0.649 15.224 7963 Z= 0.329 Chirality : 0.042 0.169 896 Planarity : 0.004 0.060 974 Dihedral : 5.080 44.716 766 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 7.19 % Allowed : 25.40 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.34), residues: 687 helix: 0.87 (0.27), residues: 408 sheet: 0.99 (1.29), residues: 17 loop : -2.08 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.034 0.002 TYR A 193 PHE 0.026 0.001 PHE A 140 TRP 0.015 0.001 TRP A 479 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5858) covalent geometry : angle 0.64889 ( 7961) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.48646 ( 2) hydrogen bonds : bond 0.04251 ( 318) hydrogen bonds : angle 4.89557 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 VAL cc_start: 0.6892 (p) cc_final: 0.6065 (m) REVERT: A 411 ILE cc_start: 0.7260 (tp) cc_final: 0.7022 (mt) REVERT: A 433 ASP cc_start: 0.4421 (OUTLIER) cc_final: 0.3438 (p0) REVERT: A 437 VAL cc_start: -0.2009 (OUTLIER) cc_final: -0.2811 (m) REVERT: A 500 VAL cc_start: 0.7065 (p) cc_final: 0.6817 (t) REVERT: A 536 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6084 (mp) REVERT: A 598 TYR cc_start: 0.7473 (m-80) cc_final: 0.6325 (m-80) REVERT: A 604 VAL cc_start: 0.8222 (t) cc_final: 0.7997 (t) REVERT: A 608 VAL cc_start: 0.7800 (t) cc_final: 0.7545 (p) REVERT: A 646 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.3981 (pp) REVERT: A 664 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6177 (mt) REVERT: A 688 MET cc_start: 0.5479 (tpp) cc_final: 0.5159 (tpp) REVERT: A 690 SER cc_start: 0.7743 (t) cc_final: 0.7111 (p) outliers start: 45 outliers final: 23 residues processed: 144 average time/residue: 0.0590 time to fit residues: 11.6948 Evaluate side-chains 132 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 703 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 55 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 657 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.239815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.205564 restraints weight = 10731.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.208843 restraints weight = 5559.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.211529 restraints weight = 3748.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.213061 restraints weight = 2922.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.213854 restraints weight = 2511.171| |-----------------------------------------------------------------------------| r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5859 Z= 0.168 Angle : 0.686 14.222 7963 Z= 0.351 Chirality : 0.044 0.169 896 Planarity : 0.005 0.060 974 Dihedral : 4.971 32.817 764 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.87 % Allowed : 25.88 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.33), residues: 687 helix: 0.69 (0.27), residues: 414 sheet: 0.46 (1.20), residues: 17 loop : -2.04 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 400 TYR 0.039 0.002 TYR A 193 PHE 0.032 0.002 PHE A 168 TRP 0.016 0.001 TRP A 668 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5858) covalent geometry : angle 0.68557 ( 7961) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.47893 ( 2) hydrogen bonds : bond 0.04465 ( 318) hydrogen bonds : angle 4.94430 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 THR cc_start: 0.7158 (p) cc_final: 0.6958 (t) REVERT: A 433 ASP cc_start: 0.4362 (OUTLIER) cc_final: 0.3043 (p0) REVERT: A 437 VAL cc_start: -0.2148 (OUTLIER) cc_final: -0.3023 (m) REVERT: A 479 TRP cc_start: 0.6204 (m100) cc_final: 0.5413 (m100) REVERT: A 598 TYR cc_start: 0.7515 (m-80) cc_final: 0.6297 (m-80) REVERT: A 608 VAL cc_start: 0.7761 (t) cc_final: 0.7547 (p) REVERT: A 646 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.4388 (pp) REVERT: A 664 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6307 (mt) outliers start: 43 outliers final: 30 residues processed: 137 average time/residue: 0.0573 time to fit residues: 10.5810 Evaluate side-chains 139 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.239540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.205174 restraints weight = 10854.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.209433 restraints weight = 5513.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.211924 restraints weight = 3511.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.212460 restraints weight = 2703.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.212460 restraints weight = 2464.480| |-----------------------------------------------------------------------------| r_work (final): 0.4625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5859 Z= 0.157 Angle : 0.691 15.217 7963 Z= 0.349 Chirality : 0.043 0.170 896 Planarity : 0.005 0.062 974 Dihedral : 4.915 33.108 764 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 7.19 % Allowed : 27.00 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.33), residues: 687 helix: 0.74 (0.27), residues: 411 sheet: 0.79 (1.24), residues: 17 loop : -2.03 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 400 TYR 0.038 0.002 TYR A 193 PHE 0.027 0.001 PHE A 140 TRP 0.016 0.001 TRP A 479 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5858) covalent geometry : angle 0.69081 ( 7961) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.47525 ( 2) hydrogen bonds : bond 0.04336 ( 318) hydrogen bonds : angle 4.91897 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.6600 (t80) cc_final: 0.6043 (t80) REVERT: A 433 ASP cc_start: 0.4186 (OUTLIER) cc_final: 0.3016 (p0) REVERT: A 437 VAL cc_start: -0.2293 (OUTLIER) cc_final: -0.3148 (m) REVERT: A 522 TYR cc_start: 0.1318 (OUTLIER) cc_final: -0.0555 (m-80) REVERT: A 598 TYR cc_start: 0.7493 (m-80) cc_final: 0.6180 (m-80) REVERT: A 646 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.4471 (pp) REVERT: A 664 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6292 (mt) outliers start: 45 outliers final: 29 residues processed: 141 average time/residue: 0.0565 time to fit residues: 10.8430 Evaluate side-chains 137 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.0040 chunk 59 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 197 ASN A 657 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.238815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.204976 restraints weight = 10714.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.208899 restraints weight = 5473.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.210654 restraints weight = 3529.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.212416 restraints weight = 2834.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.213108 restraints weight = 2436.737| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5859 Z= 0.156 Angle : 0.703 15.410 7963 Z= 0.355 Chirality : 0.043 0.164 896 Planarity : 0.005 0.061 974 Dihedral : 4.938 33.000 764 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 7.83 % Allowed : 26.84 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.33), residues: 687 helix: 0.82 (0.27), residues: 405 sheet: 0.50 (1.16), residues: 17 loop : -2.05 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 400 TYR 0.038 0.002 TYR A 193 PHE 0.024 0.001 PHE A 140 TRP 0.015 0.001 TRP A 479 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5858) covalent geometry : angle 0.70295 ( 7961) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.47847 ( 2) hydrogen bonds : bond 0.04383 ( 318) hydrogen bonds : angle 4.90217 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7200 (OUTLIER) cc_final: 0.6958 (t) REVERT: A 271 MET cc_start: 0.3356 (OUTLIER) cc_final: 0.3122 (tpt) REVERT: A 433 ASP cc_start: 0.4138 (OUTLIER) cc_final: 0.2910 (p0) REVERT: A 437 VAL cc_start: -0.1972 (OUTLIER) cc_final: -0.2896 (m) REVERT: A 522 TYR cc_start: 0.1246 (OUTLIER) cc_final: -0.0366 (m-80) REVERT: A 598 TYR cc_start: 0.7458 (m-80) cc_final: 0.6040 (m-80) REVERT: A 646 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.4525 (pp) REVERT: A 664 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6271 (mt) REVERT: A 671 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 690 SER cc_start: 0.7829 (t) cc_final: 0.7086 (p) outliers start: 49 outliers final: 30 residues processed: 138 average time/residue: 0.0690 time to fit residues: 12.7813 Evaluate side-chains 140 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 197 ASN ** 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 = 0.4866 r_free = 0.4866 target = 0.237140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.203025 restraints weight = 10724.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.206957 restraints weight = 5464.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.209527 restraints weight = 3556.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.210310 restraints weight = 2763.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.210310 restraints weight = 2478.132| |-----------------------------------------------------------------------------| r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5859 Z= 0.198 Angle : 0.758 15.673 7963 Z= 0.387 Chirality : 0.045 0.173 896 Planarity : 0.005 0.062 974 Dihedral : 5.099 33.045 764 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 7.51 % Allowed : 27.32 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.33), residues: 687 helix: 0.57 (0.26), residues: 411 sheet: 0.25 (1.11), residues: 17 loop : -2.25 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 58 TYR 0.026 0.002 TYR A 315 PHE 0.022 0.002 PHE A 140 TRP 0.018 0.002 TRP A 479 HIS 0.007 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 5858) covalent geometry : angle 0.75850 ( 7961) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.45858 ( 2) hydrogen bonds : bond 0.04737 ( 318) hydrogen bonds : angle 5.09897 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6989 (t) REVERT: A 172 THR cc_start: 0.8049 (t) cc_final: 0.7671 (p) REVERT: A 433 ASP cc_start: 0.4068 (OUTLIER) cc_final: 0.2680 (p0) REVERT: A 437 VAL cc_start: -0.2634 (OUTLIER) cc_final: -0.3545 (m) REVERT: A 522 TYR cc_start: 0.1091 (OUTLIER) cc_final: -0.0514 (m-80) REVERT: A 598 TYR cc_start: 0.7470 (m-80) cc_final: 0.5925 (m-80) REVERT: A 664 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6424 (mt) REVERT: A 671 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6884 (t80) REVERT: A 690 SER cc_start: 0.7864 (t) cc_final: 0.7103 (p) outliers start: 47 outliers final: 32 residues processed: 143 average time/residue: 0.0673 time to fit residues: 13.1592 Evaluate side-chains 142 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 0.0370 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.0020 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN A 657 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.240449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.206533 restraints weight = 10642.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.210366 restraints weight = 5427.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.212966 restraints weight = 3498.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.213645 restraints weight = 2688.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.214451 restraints weight = 2437.082| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5859 Z= 0.141 Angle : 0.736 15.473 7963 Z= 0.366 Chirality : 0.044 0.199 896 Planarity : 0.005 0.061 974 Dihedral : 4.924 33.286 764 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.39 % Allowed : 28.91 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.33), residues: 687 helix: 0.77 (0.27), residues: 404 sheet: 0.43 (1.13), residues: 17 loop : -2.00 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 58 TYR 0.023 0.002 TYR A 625 PHE 0.026 0.001 PHE A 140 TRP 0.016 0.001 TRP A 479 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5858) covalent geometry : angle 0.73644 ( 7961) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.46903 ( 2) hydrogen bonds : bond 0.04491 ( 318) hydrogen bonds : angle 4.94517 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6940 (t) REVERT: A 433 ASP cc_start: 0.3898 (OUTLIER) cc_final: 0.2873 (p0) REVERT: A 437 VAL cc_start: -0.2223 (OUTLIER) cc_final: -0.3102 (m) REVERT: A 522 TYR cc_start: 0.1189 (OUTLIER) cc_final: -0.0382 (m-80) REVERT: A 598 TYR cc_start: 0.7326 (m-80) cc_final: 0.5879 (m-80) REVERT: A 664 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6305 (mt) REVERT: A 671 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6962 (t80) REVERT: A 690 SER cc_start: 0.7777 (t) cc_final: 0.7060 (p) outliers start: 40 outliers final: 25 residues processed: 132 average time/residue: 0.0687 time to fit residues: 12.3515 Evaluate side-chains 128 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 703 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.238965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.204806 restraints weight = 10726.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.208700 restraints weight = 5451.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.211292 restraints weight = 3529.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.211954 restraints weight = 2714.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.211954 restraints weight = 2455.784| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5859 Z= 0.164 Angle : 0.757 15.623 7963 Z= 0.378 Chirality : 0.045 0.197 896 Planarity : 0.005 0.061 974 Dihedral : 4.722 33.542 762 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.39 % Allowed : 28.91 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.33), residues: 687 helix: 0.73 (0.27), residues: 398 sheet: 0.42 (1.12), residues: 17 loop : -1.95 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.023 0.002 TYR A 193 PHE 0.025 0.001 PHE A 140 TRP 0.016 0.001 TRP A 668 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5858) covalent geometry : angle 0.75709 ( 7961) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.46385 ( 2) hydrogen bonds : bond 0.04600 ( 318) hydrogen bonds : angle 4.99623 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6930 (t) REVERT: A 172 THR cc_start: 0.8047 (t) cc_final: 0.7722 (p) REVERT: A 433 ASP cc_start: 0.3887 (OUTLIER) cc_final: 0.2650 (p0) REVERT: A 437 VAL cc_start: -0.2308 (OUTLIER) cc_final: -0.3181 (m) REVERT: A 522 TYR cc_start: 0.1108 (OUTLIER) cc_final: -0.0765 (m-80) REVERT: A 598 TYR cc_start: 0.7331 (m-80) cc_final: 0.5869 (m-80) REVERT: A 664 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6304 (mt) REVERT: A 671 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7030 (t80) REVERT: A 683 ILE cc_start: 0.7953 (tp) cc_final: 0.7453 (tt) REVERT: A 690 SER cc_start: 0.7803 (t) cc_final: 0.7123 (p) outliers start: 40 outliers final: 30 residues processed: 132 average time/residue: 0.0741 time to fit residues: 13.2842 Evaluate side-chains 136 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.238832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.204483 restraints weight = 10642.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.208395 restraints weight = 5441.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.210822 restraints weight = 3522.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.211555 restraints weight = 2763.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.211555 restraints weight = 2494.152| |-----------------------------------------------------------------------------| r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5859 Z= 0.164 Angle : 0.773 15.814 7963 Z= 0.383 Chirality : 0.045 0.205 896 Planarity : 0.005 0.062 974 Dihedral : 4.724 33.823 762 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.07 % Allowed : 29.71 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.33), residues: 687 helix: 0.72 (0.27), residues: 398 sheet: 0.52 (1.15), residues: 17 loop : -1.93 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.023 0.002 TYR A 193 PHE 0.026 0.001 PHE A 140 TRP 0.017 0.001 TRP A 479 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5858) covalent geometry : angle 0.77276 ( 7961) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.46460 ( 2) hydrogen bonds : bond 0.04626 ( 318) hydrogen bonds : angle 4.96304 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6943 (t) REVERT: A 172 THR cc_start: 0.8050 (t) cc_final: 0.7731 (p) REVERT: A 433 ASP cc_start: 0.3885 (OUTLIER) cc_final: 0.2697 (p0) REVERT: A 437 VAL cc_start: -0.2365 (OUTLIER) cc_final: -0.3226 (m) REVERT: A 522 TYR cc_start: 0.1113 (OUTLIER) cc_final: -0.0470 (m-80) REVERT: A 598 TYR cc_start: 0.7285 (m-80) cc_final: 0.5852 (m-80) REVERT: A 664 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6290 (mt) REVERT: A 671 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 690 SER cc_start: 0.7734 (t) cc_final: 0.7068 (p) outliers start: 38 outliers final: 29 residues processed: 131 average time/residue: 0.0594 time to fit residues: 10.5947 Evaluate side-chains 136 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.239201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.204781 restraints weight = 10588.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.208554 restraints weight = 5544.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.211097 restraints weight = 3650.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.211815 restraints weight = 2860.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.211815 restraints weight = 2589.583| |-----------------------------------------------------------------------------| r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5859 Z= 0.166 Angle : 0.764 15.784 7963 Z= 0.382 Chirality : 0.045 0.197 896 Planarity : 0.005 0.061 974 Dihedral : 4.752 33.620 762 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.71 % Allowed : 29.07 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.33), residues: 687 helix: 0.70 (0.27), residues: 398 sheet: 0.50 (1.14), residues: 17 loop : -1.95 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.024 0.002 TYR A 193 PHE 0.026 0.001 PHE A 140 TRP 0.017 0.001 TRP A 479 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5858) covalent geometry : angle 0.76420 ( 7961) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.46370 ( 2) hydrogen bonds : bond 0.04661 ( 318) hydrogen bonds : angle 5.01728 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1158.08 seconds wall clock time: 20 minutes 40.24 seconds (1240.24 seconds total)