Starting phenix.real_space_refine on Wed Mar 4 10:30:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbu_32406/03_2026/7wbu_32406.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbu_32406/03_2026/7wbu_32406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wbu_32406/03_2026/7wbu_32406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbu_32406/03_2026/7wbu_32406.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbu_32406/03_2026/7wbu_32406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbu_32406/03_2026/7wbu_32406.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7170 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 77 5.16 5 C 4558 2.51 5 N 1189 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7170 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7143 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 868} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.26 Number of scatterers: 7170 At special positions: 0 Unit cell: (84.66, 90.885, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 2 15.00 O 1344 8.00 N 1189 7.00 C 4558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 275.7 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 57.1% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 97 through 112 removed outlier: 3.921A pdb=" N GLU A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 191 through 196 removed outlier: 4.075A pdb=" N GLY A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 303 through 315 Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.810A pdb=" N LYS A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 388 through 409 Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 449 through 461 removed outlier: 3.829A pdb=" N TYR A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 492 through 504 removed outlier: 3.833A pdb=" N THR A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 516 Processing helix chain 'A' and resid 522 through 537 Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.653A pdb=" N VAL A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 3.761A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 615 through 633 removed outlier: 4.029A pdb=" N ALA A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 631 " --> pdb=" O CYS A 627 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 659 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 703 through 715 Processing helix chain 'A' and resid 732 through 746 removed outlier: 3.989A pdb=" N ASP A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 816 through 829 removed outlier: 4.213A pdb=" N VAL A 821 " --> pdb=" O LYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.546A pdb=" N ILE A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 887 Processing helix chain 'A' and resid 905 through 915 removed outlier: 4.411A pdb=" N ASP A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 944 Processing helix chain 'A' and resid 960 through 974 Processing helix chain 'A' and resid 984 through 993 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.035A pdb=" N PHE A 185 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 230 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 187 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASP A 232 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 189 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 278 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 152 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 576 removed outlier: 4.432A pdb=" N MET A 602 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 639 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASN A 671 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 641 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE A 668 " --> pdb=" O ASN A 696 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.80 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: 1196 1.31 - 1.44: 1881 1.44 - 1.56: 4134 1.56 - 1.69: 5 1.69 - 1.82: 103 Bond restraints: 7319 Sorted by residual: bond pdb=" C ASN A 615 " pdb=" O ASN A 615 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" C LYS A 619 " pdb=" O LYS A 619 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.61e+01 bond pdb=" C GLU A 618 " pdb=" O GLU A 618 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.17e-02 7.31e+03 1.58e+01 bond pdb=" CA LYS A 619 " pdb=" C LYS A 619 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.27e-02 6.20e+03 1.52e+01 bond pdb=" N LYS A 619 " pdb=" CA LYS A 619 " ideal model delta sigma weight residual 1.459 1.425 0.035 1.19e-02 7.06e+03 8.52e+00 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 9746 1.98 - 3.96: 113 3.96 - 5.95: 28 5.95 - 7.93: 9 7.93 - 9.91: 2 Bond angle restraints: 9898 Sorted by residual: angle pdb=" CA PRO A 98 " pdb=" N PRO A 98 " pdb=" CD PRO A 98 " ideal model delta sigma weight residual 112.00 102.09 9.91 1.40e+00 5.10e-01 5.01e+01 angle pdb=" CA PRO A 254 " pdb=" N PRO A 254 " pdb=" CD PRO A 254 " ideal model delta sigma weight residual 112.00 104.23 7.77 1.40e+00 5.10e-01 3.08e+01 angle pdb=" N ASN A 615 " pdb=" CA ASN A 615 " pdb=" CB ASN A 615 " ideal model delta sigma weight residual 110.49 119.62 -9.13 1.69e+00 3.50e-01 2.92e+01 angle pdb=" N THR A 616 " pdb=" CA THR A 616 " pdb=" C THR A 616 " ideal model delta sigma weight residual 111.28 116.43 -5.15 1.09e+00 8.42e-01 2.23e+01 angle pdb=" N GLU A 454 " pdb=" CA GLU A 454 " pdb=" CB GLU A 454 " ideal model delta sigma weight residual 110.39 116.67 -6.28 1.66e+00 3.63e-01 1.43e+01 ... (remaining 9893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 4192 26.27 - 52.54: 220 52.54 - 78.81: 16 78.81 - 105.08: 6 105.08 - 131.35: 2 Dihedral angle restraints: 4436 sinusoidal: 1793 harmonic: 2643 Sorted by residual: dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 168.65 131.35 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 176.19 123.81 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" N ASN A 615 " pdb=" C ASN A 615 " pdb=" CA ASN A 615 " pdb=" CB ASN A 615 " ideal model delta harmonic sigma weight residual 122.80 132.69 -9.89 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 4433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 967 0.055 - 0.110: 149 0.110 - 0.164: 11 0.164 - 0.219: 0 0.219 - 0.274: 3 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CA THR A 616 " pdb=" N THR A 616 " pdb=" C THR A 616 " pdb=" CB THR A 616 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASN A 615 " pdb=" N ASN A 615 " pdb=" C ASN A 615 " pdb=" CB ASN A 615 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO A 98 " pdb=" N PRO A 98 " pdb=" C PRO A 98 " pdb=" CB PRO A 98 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1127 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 253 " 0.096 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO A 254 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 97 " 0.065 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 98 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.015 2.00e-02 2.50e+03 1.62e-02 6.56e+00 pdb=" CG TRP A 432 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " -0.000 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 126 2.70 - 3.25: 7093 3.25 - 3.80: 11243 3.80 - 4.35: 14609 4.35 - 4.90: 23944 Nonbonded interactions: 57015 Sorted by model distance: nonbonded pdb=" O VAL A 605 " pdb=" NZ LYS A 619 " model vdw 2.145 3.120 nonbonded pdb=" OD1 ASP A 875 " pdb=" OG SER A 906 " model vdw 2.249 3.040 nonbonded pdb=" NE1 TRP A 210 " pdb=" OG SER A 214 " model vdw 2.256 3.120 nonbonded pdb=" O LEU A 309 " pdb=" ND1 HIS A 313 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" O VAL A 186 " model vdw 2.327 3.040 ... (remaining 57010 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.720 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 7319 Z= 0.180 Angle : 0.590 9.912 9898 Z= 0.314 Chirality : 0.040 0.274 1130 Planarity : 0.006 0.140 1248 Dihedral : 15.373 131.352 2706 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.37 % Allowed : 0.24 % Favored : 99.39 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.29), residues: 894 helix: 1.57 (0.24), residues: 476 sheet: -0.68 (0.53), residues: 109 loop : -0.38 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.013 0.001 TYR A 139 PHE 0.017 0.001 PHE A 107 TRP 0.043 0.002 TRP A 432 HIS 0.003 0.001 HIS A 887 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7319) covalent geometry : angle 0.59009 ( 9898) hydrogen bonds : bond 0.13141 ( 366) hydrogen bonds : angle 5.53709 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.267 Fit side-chains REVERT: A 417 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6995 (tm-30) REVERT: A 578 THR cc_start: 0.7833 (m) cc_final: 0.7529 (p) outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 0.0690 time to fit residues: 14.3402 Evaluate side-chains 102 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 287 ASN A 675 ASN A 678 ASN A 803 ASN ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.173864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.148381 restraints weight = 10004.653| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.55 r_work: 0.3717 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7319 Z= 0.165 Angle : 0.584 8.165 9898 Z= 0.295 Chirality : 0.040 0.141 1130 Planarity : 0.005 0.082 1248 Dihedral : 7.397 136.578 960 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.59 % Allowed : 9.28 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.29), residues: 894 helix: 1.49 (0.24), residues: 488 sheet: -0.89 (0.52), residues: 115 loop : -0.31 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 510 TYR 0.010 0.001 TYR A 288 PHE 0.022 0.002 PHE A 107 TRP 0.020 0.002 TRP A 432 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7319) covalent geometry : angle 0.58366 ( 9898) hydrogen bonds : bond 0.03682 ( 366) hydrogen bonds : angle 4.28476 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 107 PHE cc_start: 0.7414 (m-80) cc_final: 0.7090 (m-80) REVERT: A 124 TYR cc_start: 0.7647 (t80) cc_final: 0.6869 (t80) REVERT: A 407 MET cc_start: 0.8371 (mmm) cc_final: 0.8123 (mmm) REVERT: A 417 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 725 MET cc_start: 0.8113 (mtt) cc_final: 0.7903 (mtt) REVERT: A 843 CYS cc_start: 0.7381 (m) cc_final: 0.6965 (m) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.0788 time to fit residues: 14.3435 Evaluate side-chains 109 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 803 ASN A 887 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.169797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143876 restraints weight = 9870.417| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.55 r_work: 0.3657 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7319 Z= 0.185 Angle : 0.590 6.900 9898 Z= 0.298 Chirality : 0.041 0.154 1130 Planarity : 0.004 0.067 1248 Dihedral : 7.478 145.423 957 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.32 % Allowed : 10.74 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.29), residues: 894 helix: 1.45 (0.23), residues: 486 sheet: -1.01 (0.52), residues: 109 loop : -0.48 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.011 0.001 TYR A 124 PHE 0.033 0.002 PHE A 107 TRP 0.012 0.001 TRP A 494 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7319) covalent geometry : angle 0.59001 ( 9898) hydrogen bonds : bond 0.03951 ( 366) hydrogen bonds : angle 4.26721 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.272 Fit side-chains REVERT: A 117 LEU cc_start: 0.7980 (pt) cc_final: 0.7760 (tt) REVERT: A 284 MET cc_start: 0.1380 (ttt) cc_final: 0.0600 (tmm) REVERT: A 581 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6883 (mm-30) REVERT: A 725 MET cc_start: 0.8015 (mtt) cc_final: 0.7732 (mtt) REVERT: A 961 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6907 (mp0) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.0681 time to fit residues: 12.0104 Evaluate side-chains 104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 529 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.169361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143419 restraints weight = 10167.762| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.65 r_work: 0.3629 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7319 Z= 0.178 Angle : 0.582 7.047 9898 Z= 0.294 Chirality : 0.040 0.147 1130 Planarity : 0.004 0.060 1248 Dihedral : 7.542 151.233 957 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.56 % Allowed : 13.68 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.29), residues: 894 helix: 1.45 (0.23), residues: 484 sheet: -1.25 (0.52), residues: 113 loop : -0.46 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 590 TYR 0.014 0.001 TYR A 124 PHE 0.016 0.002 PHE A 107 TRP 0.014 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 7319) covalent geometry : angle 0.58208 ( 9898) hydrogen bonds : bond 0.03778 ( 366) hydrogen bonds : angle 4.24865 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.171 Fit side-chains REVERT: A 124 TYR cc_start: 0.7593 (t80) cc_final: 0.7365 (t80) REVERT: A 284 MET cc_start: 0.1280 (ttt) cc_final: 0.0580 (tmm) REVERT: A 371 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 407 MET cc_start: 0.8282 (mmm) cc_final: 0.8071 (mmm) REVERT: A 474 ILE cc_start: 0.9330 (mt) cc_final: 0.9113 (mm) REVERT: A 581 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7000 (mm-30) REVERT: A 590 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7379 (ttp-170) REVERT: A 725 MET cc_start: 0.8020 (mtt) cc_final: 0.7770 (mtt) REVERT: A 961 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6904 (mp0) outliers start: 21 outliers final: 14 residues processed: 119 average time/residue: 0.0683 time to fit residues: 11.3867 Evaluate side-chains 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 80 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.171445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144772 restraints weight = 10005.181| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.70 r_work: 0.3661 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7319 Z= 0.132 Angle : 0.539 7.051 9898 Z= 0.273 Chirality : 0.039 0.148 1130 Planarity : 0.004 0.046 1248 Dihedral : 7.577 167.621 957 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 15.02 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 894 helix: 1.54 (0.24), residues: 486 sheet: -1.13 (0.53), residues: 109 loop : -0.47 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.011 0.001 TYR A 124 PHE 0.035 0.002 PHE A 107 TRP 0.010 0.001 TRP A 494 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7319) covalent geometry : angle 0.53905 ( 9898) hydrogen bonds : bond 0.03382 ( 366) hydrogen bonds : angle 4.11629 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.284 Fit side-chains REVERT: A 124 TYR cc_start: 0.7457 (t80) cc_final: 0.7246 (t80) REVERT: A 284 MET cc_start: 0.1590 (ttt) cc_final: 0.1009 (tmm) REVERT: A 325 PHE cc_start: 0.7682 (t80) cc_final: 0.7441 (t80) REVERT: A 371 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 407 MET cc_start: 0.8414 (mmm) cc_final: 0.8126 (mmm) REVERT: A 474 ILE cc_start: 0.9322 (mt) cc_final: 0.9109 (mm) REVERT: A 581 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7085 (mm-30) REVERT: A 725 MET cc_start: 0.7984 (mtt) cc_final: 0.7661 (mtt) REVERT: A 961 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6830 (mp0) outliers start: 20 outliers final: 13 residues processed: 120 average time/residue: 0.0650 time to fit residues: 11.4547 Evaluate side-chains 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.167007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140807 restraints weight = 10111.776| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.12 r_work: 0.3582 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7319 Z= 0.212 Angle : 0.627 6.662 9898 Z= 0.319 Chirality : 0.041 0.155 1130 Planarity : 0.004 0.052 1248 Dihedral : 7.071 153.014 957 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.17 % Allowed : 16.00 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.29), residues: 894 helix: 1.30 (0.23), residues: 484 sheet: -1.38 (0.52), residues: 112 loop : -0.53 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.018 0.002 TYR A 124 PHE 0.030 0.002 PHE A 107 TRP 0.011 0.002 TRP A 494 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7319) covalent geometry : angle 0.62726 ( 9898) hydrogen bonds : bond 0.04098 ( 366) hydrogen bonds : angle 4.45863 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.282 Fit side-chains REVERT: A 371 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8516 (tt) REVERT: A 437 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7534 (mp) REVERT: A 688 HIS cc_start: 0.4960 (OUTLIER) cc_final: 0.4607 (t-90) REVERT: A 961 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6895 (mp0) REVERT: A 973 MET cc_start: 0.5911 (mtp) cc_final: 0.5649 (mtp) outliers start: 26 outliers final: 16 residues processed: 119 average time/residue: 0.0624 time to fit residues: 10.9306 Evaluate side-chains 109 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN A 887 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.172783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146819 restraints weight = 10012.164| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.64 r_work: 0.3669 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7319 Z= 0.102 Angle : 0.549 6.851 9898 Z= 0.275 Chirality : 0.038 0.146 1130 Planarity : 0.004 0.049 1248 Dihedral : 5.374 97.803 957 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 16.85 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.29), residues: 894 helix: 1.52 (0.24), residues: 486 sheet: -1.28 (0.52), residues: 108 loop : -0.38 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.009 0.001 TYR A 698 PHE 0.027 0.001 PHE A 107 TRP 0.010 0.001 TRP A 494 HIS 0.004 0.001 HIS A 887 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7319) covalent geometry : angle 0.54896 ( 9898) hydrogen bonds : bond 0.03081 ( 366) hydrogen bonds : angle 4.16642 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.291 Fit side-chains REVERT: A 125 GLU cc_start: 0.6802 (pt0) cc_final: 0.6482 (pt0) REVERT: A 335 PHE cc_start: 0.7750 (t80) cc_final: 0.7483 (t80) REVERT: A 407 MET cc_start: 0.8436 (mmm) cc_final: 0.8193 (mmm) REVERT: A 431 MET cc_start: 0.8648 (tmm) cc_final: 0.8400 (tmm) REVERT: A 437 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7560 (mp) REVERT: A 581 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7221 (mm-30) REVERT: A 590 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7433 (ttp-170) REVERT: A 725 MET cc_start: 0.8080 (mtt) cc_final: 0.7831 (mtt) REVERT: A 961 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6818 (mp0) REVERT: A 973 MET cc_start: 0.5779 (mtp) cc_final: 0.5530 (mtp) outliers start: 21 outliers final: 11 residues processed: 120 average time/residue: 0.0741 time to fit residues: 12.7747 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 887 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.172715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.147268 restraints weight = 9952.483| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.60 r_work: 0.3675 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7319 Z= 0.105 Angle : 0.566 14.286 9898 Z= 0.280 Chirality : 0.038 0.172 1130 Planarity : 0.003 0.048 1248 Dihedral : 5.160 92.297 957 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.32 % Allowed : 17.58 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.29), residues: 894 helix: 1.53 (0.24), residues: 491 sheet: -1.13 (0.52), residues: 109 loop : -0.31 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.009 0.001 TYR A 124 PHE 0.022 0.001 PHE A 107 TRP 0.010 0.001 TRP A 927 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7319) covalent geometry : angle 0.56617 ( 9898) hydrogen bonds : bond 0.03011 ( 366) hydrogen bonds : angle 4.13791 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.292 Fit side-chains REVERT: A 407 MET cc_start: 0.8217 (mmm) cc_final: 0.7975 (mmm) REVERT: A 431 MET cc_start: 0.8567 (tmm) cc_final: 0.8310 (tmm) REVERT: A 437 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7498 (mp) REVERT: A 581 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 590 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7419 (ttp-170) REVERT: A 725 MET cc_start: 0.8064 (mtt) cc_final: 0.7791 (mtt) REVERT: A 961 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6883 (mp0) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.0750 time to fit residues: 12.1711 Evaluate side-chains 104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.172240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146499 restraints weight = 9771.402| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.62 r_work: 0.3708 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7319 Z= 0.102 Angle : 0.564 13.365 9898 Z= 0.279 Chirality : 0.038 0.150 1130 Planarity : 0.004 0.084 1248 Dihedral : 4.987 86.778 957 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.83 % Allowed : 17.83 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 894 helix: 1.53 (0.24), residues: 492 sheet: -1.22 (0.52), residues: 108 loop : -0.26 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.008 0.001 TYR A 310 PHE 0.026 0.001 PHE A 325 TRP 0.008 0.001 TRP A 623 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7319) covalent geometry : angle 0.56436 ( 9898) hydrogen bonds : bond 0.02954 ( 366) hydrogen bonds : angle 4.12825 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.267 Fit side-chains REVERT: A 124 TYR cc_start: 0.6941 (t80) cc_final: 0.6524 (t80) REVERT: A 284 MET cc_start: 0.1516 (ttt) cc_final: 0.0546 (tmm) REVERT: A 407 MET cc_start: 0.8212 (mmm) cc_final: 0.7954 (mmm) REVERT: A 431 MET cc_start: 0.8566 (tmm) cc_final: 0.8315 (tmm) REVERT: A 437 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 590 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7454 (ttp-170) REVERT: A 711 CYS cc_start: 0.7933 (m) cc_final: 0.7693 (m) REVERT: A 725 MET cc_start: 0.8003 (mtt) cc_final: 0.7736 (mtt) outliers start: 15 outliers final: 12 residues processed: 105 average time/residue: 0.0786 time to fit residues: 11.5959 Evaluate side-chains 103 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.173169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147353 restraints weight = 9833.806| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.65 r_work: 0.3715 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7319 Z= 0.100 Angle : 0.577 13.211 9898 Z= 0.281 Chirality : 0.038 0.147 1130 Planarity : 0.004 0.080 1248 Dihedral : 4.792 79.166 957 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.59 % Allowed : 17.95 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.29), residues: 894 helix: 1.53 (0.24), residues: 493 sheet: -1.18 (0.52), residues: 108 loop : -0.31 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 180 TYR 0.007 0.001 TYR A 124 PHE 0.020 0.001 PHE A 188 TRP 0.008 0.001 TRP A 927 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7319) covalent geometry : angle 0.57725 ( 9898) hydrogen bonds : bond 0.02876 ( 366) hydrogen bonds : angle 4.12059 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.271 Fit side-chains REVERT: A 124 TYR cc_start: 0.6866 (t80) cc_final: 0.6545 (t80) REVERT: A 269 MET cc_start: 0.8513 (ttt) cc_final: 0.8231 (ttt) REVERT: A 284 MET cc_start: 0.1423 (ttt) cc_final: 0.0525 (tmm) REVERT: A 417 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 431 MET cc_start: 0.8582 (tmm) cc_final: 0.8338 (tmm) REVERT: A 437 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7560 (mp) REVERT: A 590 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7443 (ttp-170) REVERT: A 725 MET cc_start: 0.8107 (mtt) cc_final: 0.7827 (mtt) REVERT: A 898 GLU cc_start: 0.7483 (pm20) cc_final: 0.6929 (pp20) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.0739 time to fit residues: 11.2714 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 591 HIS Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 976 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145595 restraints weight = 9969.604| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.64 r_work: 0.3679 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7319 Z= 0.116 Angle : 0.587 13.127 9898 Z= 0.287 Chirality : 0.039 0.152 1130 Planarity : 0.004 0.080 1248 Dihedral : 4.876 78.495 957 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.95 % Allowed : 17.70 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 894 helix: 1.57 (0.24), residues: 486 sheet: -1.11 (0.52), residues: 109 loop : -0.33 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.010 0.001 TYR A 124 PHE 0.020 0.001 PHE A 325 TRP 0.008 0.001 TRP A 494 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7319) covalent geometry : angle 0.58732 ( 9898) hydrogen bonds : bond 0.03031 ( 366) hydrogen bonds : angle 4.14435 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1511.79 seconds wall clock time: 26 minutes 43.18 seconds (1603.18 seconds total)