Starting phenix.real_space_refine on Wed Jun 11 15:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbu_32406/06_2025/7wbu_32406.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbu_32406/06_2025/7wbu_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_32406/06_2025/7wbu_32406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbu_32406/06_2025/7wbu_32406.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbu_32406/06_2025/7wbu_32406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbu_32406/06_2025/7wbu_32406.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.63, per 1000 atoms: 0.65 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: 1.96 Conformation dependent library (CDL) restraints added in 899.7 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: 0.86 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: 2.21 Time building geometry restraints manager: 2.29 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- 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 : 7.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.043 0.002 TRP A 432 HIS 0.003 0.001 HIS A 887 PHE 0.017 0.001 PHE A 107 TYR 0.013 0.001 TYR A 139 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.13141 ( 366) hydrogen bonds : angle 5.53709 ( 1089) covalent geometry : bond 0.00350 ( 7319) covalent geometry : angle 0.59009 ( 9898) *********************** 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 : 0.833 Fit side-chains REVERT: A 417 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 578 THR cc_start: 0.7833 (m) cc_final: 0.7528 (p) outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 0.1631 time to fit residues: 33.2112 Evaluate side-chains 103 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.1818 ------------------------------------------------------------------------------- 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 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.178777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152920 restraints weight = 9821.813| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.61 r_work: 0.3776 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7319 Z= 0.117 Angle : 0.531 7.786 9898 Z= 0.267 Chirality : 0.038 0.137 1130 Planarity : 0.004 0.082 1248 Dihedral : 7.138 131.845 960 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.34 % Allowed : 8.30 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 894 helix: 1.67 (0.24), residues: 488 sheet: -0.78 (0.52), residues: 111 loop : -0.26 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 432 HIS 0.003 0.001 HIS A 313 PHE 0.021 0.001 PHE A 107 TYR 0.010 0.001 TYR A 288 ARG 0.004 0.000 ARG A 510 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 366) hydrogen bonds : angle 4.15555 ( 1089) covalent geometry : bond 0.00271 ( 7319) covalent geometry : angle 0.53127 ( 9898) *********************** 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 140 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 107 PHE cc_start: 0.6914 (m-80) cc_final: 0.6697 (m-10) REVERT: A 124 TYR cc_start: 0.7529 (t80) cc_final: 0.6840 (t80) REVERT: A 417 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 581 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7495 (mp0) outliers start: 11 outliers final: 9 residues processed: 135 average time/residue: 0.1685 time to fit residues: 31.8510 Evaluate side-chains 113 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 GLU 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 605 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 738 ASP 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 85 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 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 = 0.4142 r_free = 0.4142 target = 0.175213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148733 restraints weight = 9889.135| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.57 r_work: 0.3722 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1968 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= 0.138 Angle : 0.541 7.103 9898 Z= 0.273 Chirality : 0.039 0.151 1130 Planarity : 0.004 0.067 1248 Dihedral : 7.221 138.373 957 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.83 % Allowed : 9.52 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 894 helix: 1.61 (0.24), residues: 489 sheet: -0.86 (0.52), residues: 111 loop : -0.30 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.005 0.001 HIS A 313 PHE 0.023 0.002 PHE A 325 TYR 0.009 0.001 TYR A 124 ARG 0.004 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 366) hydrogen bonds : angle 4.04288 ( 1089) covalent geometry : bond 0.00321 ( 7319) covalent geometry : angle 0.54130 ( 9898) *********************** 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 129 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.772 Fit side-chains REVERT: A 417 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 581 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7516 (mp0) REVERT: A 725 MET cc_start: 0.8067 (mtt) cc_final: 0.7796 (mtt) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.1627 time to fit residues: 28.1307 Evaluate side-chains 106 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 235 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 738 ASP 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: 0.9980 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.175956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150259 restraints weight = 10009.758| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.61 r_work: 0.3716 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7319 Z= 0.105 Angle : 0.511 6.736 9898 Z= 0.257 Chirality : 0.038 0.144 1130 Planarity : 0.004 0.059 1248 Dihedral : 7.190 143.356 957 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.95 % Allowed : 12.09 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 894 helix: 1.67 (0.24), residues: 494 sheet: -0.90 (0.51), residues: 112 loop : -0.24 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.003 0.001 HIS A 155 PHE 0.023 0.001 PHE A 188 TYR 0.007 0.001 TYR A 288 ARG 0.006 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 366) hydrogen bonds : angle 3.94304 ( 1089) covalent geometry : bond 0.00240 ( 7319) covalent geometry : angle 0.51118 ( 9898) *********************** 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 130 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.841 Fit side-chains REVERT: A 124 TYR cc_start: 0.7268 (t80) cc_final: 0.6532 (t80) REVERT: A 417 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 581 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7530 (mp0) REVERT: A 725 MET cc_start: 0.8085 (mtt) cc_final: 0.7709 (mtt) REVERT: A 933 ASP cc_start: 0.6546 (m-30) cc_final: 0.6047 (p0) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 0.1589 time to fit residues: 27.9871 Evaluate side-chains 112 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL 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 62 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.170346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143504 restraints weight = 9887.219| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.71 r_work: 0.3635 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2776 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= 0.187 Angle : 0.596 6.983 9898 Z= 0.302 Chirality : 0.041 0.154 1130 Planarity : 0.004 0.047 1248 Dihedral : 7.556 153.476 957 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.81 % Allowed : 13.31 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 894 helix: 1.57 (0.24), residues: 486 sheet: -1.16 (0.52), residues: 108 loop : -0.42 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 494 HIS 0.004 0.001 HIS A 155 PHE 0.022 0.002 PHE A 107 TYR 0.016 0.001 TYR A 124 ARG 0.006 0.001 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 366) hydrogen bonds : angle 4.26354 ( 1089) covalent geometry : bond 0.00437 ( 7319) covalent geometry : angle 0.59621 ( 9898) *********************** 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 126 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.829 Fit side-chains REVERT: A 228 LEU cc_start: 0.8430 (tp) cc_final: 0.8102 (tp) REVERT: A 284 MET cc_start: 0.1260 (ttt) cc_final: 0.0570 (tmm) REVERT: A 318 LYS cc_start: 0.7239 (mppt) cc_final: 0.6835 (mppt) REVERT: A 454 GLU cc_start: 0.7502 (mp0) cc_final: 0.7241 (mp0) REVERT: A 581 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7556 (mp0) REVERT: A 961 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6932 (mp0) outliers start: 23 outliers final: 17 residues processed: 120 average time/residue: 0.1545 time to fit residues: 26.9591 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 288 TYR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR 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 843 CYS Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 906 SER 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 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.172083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146613 restraints weight = 9875.980| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.66 r_work: 0.3675 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2798 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= 0.118 Angle : 0.549 11.928 9898 Z= 0.273 Chirality : 0.039 0.148 1130 Planarity : 0.003 0.048 1248 Dihedral : 7.598 172.906 957 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.69 % Allowed : 14.16 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 894 helix: 1.63 (0.24), residues: 487 sheet: -1.17 (0.52), residues: 108 loop : -0.40 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 179 HIS 0.003 0.001 HIS A 155 PHE 0.019 0.001 PHE A 107 TYR 0.010 0.001 TYR A 124 ARG 0.003 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 366) hydrogen bonds : angle 4.11130 ( 1089) covalent geometry : bond 0.00271 ( 7319) covalent geometry : angle 0.54879 ( 9898) *********************** 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 132 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.881 Fit side-chains REVERT: A 124 TYR cc_start: 0.7567 (t80) cc_final: 0.7282 (t80) REVERT: A 228 LEU cc_start: 0.8485 (tp) cc_final: 0.8236 (tp) REVERT: A 284 MET cc_start: 0.1225 (ttt) cc_final: 0.0583 (tmm) REVERT: A 318 LYS cc_start: 0.7087 (mppt) cc_final: 0.6676 (mppt) REVERT: A 371 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 474 ILE cc_start: 0.9295 (mt) cc_final: 0.9082 (mm) REVERT: A 581 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7511 (mp0) REVERT: A 841 MET cc_start: 0.8677 (ptp) cc_final: 0.8476 (mtm) REVERT: A 933 ASP cc_start: 0.6676 (m-30) cc_final: 0.6192 (p0) REVERT: A 961 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6881 (mp0) outliers start: 22 outliers final: 12 residues processed: 124 average time/residue: 0.1558 time to fit residues: 27.8572 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 169 VAL 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 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.172680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147758 restraints weight = 9833.834| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.50 r_work: 0.3684 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7319 Z= 0.113 Angle : 0.547 9.844 9898 Z= 0.275 Chirality : 0.038 0.144 1130 Planarity : 0.004 0.053 1248 Dihedral : 6.271 136.016 957 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 15.51 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 894 helix: 1.64 (0.24), residues: 487 sheet: -1.08 (0.52), residues: 108 loop : -0.37 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.003 0.001 HIS A 155 PHE 0.024 0.001 PHE A 325 TYR 0.009 0.001 TYR A 124 ARG 0.002 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 366) hydrogen bonds : angle 4.11404 ( 1089) covalent geometry : bond 0.00258 ( 7319) covalent geometry : angle 0.54698 ( 9898) *********************** 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 124 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.789 Fit side-chains REVERT: A 125 GLU cc_start: 0.6763 (pt0) cc_final: 0.6524 (pt0) REVERT: A 318 LYS cc_start: 0.6988 (mppt) cc_final: 0.6622 (mppt) REVERT: A 371 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8663 (tt) REVERT: A 454 GLU cc_start: 0.7689 (mp0) cc_final: 0.7467 (mp0) REVERT: A 474 ILE cc_start: 0.9296 (mt) cc_final: 0.9076 (mm) REVERT: A 581 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7532 (mp0) REVERT: A 711 CYS cc_start: 0.7896 (m) cc_final: 0.7619 (m) REVERT: A 898 GLU cc_start: 0.7484 (pm20) cc_final: 0.7009 (pp20) REVERT: A 933 ASP cc_start: 0.6741 (m-30) cc_final: 0.6241 (p0) outliers start: 20 outliers final: 16 residues processed: 118 average time/residue: 0.1537 time to fit residues: 26.1339 Evaluate side-chains 107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 605 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.168952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143432 restraints weight = 10018.899| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.61 r_work: 0.3637 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7319 Z= 0.184 Angle : 0.618 10.647 9898 Z= 0.310 Chirality : 0.041 0.155 1130 Planarity : 0.004 0.048 1248 Dihedral : 5.637 103.247 957 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.93 % Allowed : 15.87 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 894 helix: 1.47 (0.23), residues: 485 sheet: -1.10 (0.53), residues: 108 loop : -0.47 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 PHE 0.028 0.002 PHE A 107 TYR 0.015 0.001 TYR A 124 ARG 0.004 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 366) hydrogen bonds : angle 4.37903 ( 1089) covalent geometry : bond 0.00435 ( 7319) covalent geometry : angle 0.61844 ( 9898) *********************** 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 121 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.882 Fit side-chains REVERT: A 124 TYR cc_start: 0.7870 (t80) cc_final: 0.7657 (t80) REVERT: A 125 GLU cc_start: 0.6979 (pt0) cc_final: 0.6729 (pt0) REVERT: A 318 LYS cc_start: 0.7156 (mppt) cc_final: 0.6824 (mptt) REVERT: A 371 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8476 (tt) REVERT: A 474 ILE cc_start: 0.9331 (mt) cc_final: 0.9129 (mm) REVERT: A 688 HIS cc_start: 0.4752 (OUTLIER) cc_final: 0.4509 (t-90) REVERT: A 961 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6828 (mp0) outliers start: 24 outliers final: 16 residues processed: 114 average time/residue: 0.1745 time to fit residues: 28.5370 Evaluate side-chains 112 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 228 LEU 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 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN A 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142186 restraints weight = 10011.722| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.60 r_work: 0.3618 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7319 Z= 0.185 Angle : 0.626 10.351 9898 Z= 0.313 Chirality : 0.041 0.150 1130 Planarity : 0.004 0.048 1248 Dihedral : 5.801 107.897 957 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.93 % Allowed : 15.87 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.28), residues: 894 helix: 1.41 (0.23), residues: 485 sheet: -1.21 (0.53), residues: 108 loop : -0.52 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 179 HIS 0.004 0.001 HIS A 155 PHE 0.029 0.002 PHE A 107 TYR 0.014 0.001 TYR A 124 ARG 0.004 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 366) hydrogen bonds : angle 4.44495 ( 1089) covalent geometry : bond 0.00437 ( 7319) covalent geometry : angle 0.62567 ( 9898) *********************** 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 123 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.784 Fit side-chains REVERT: A 125 GLU cc_start: 0.6982 (pt0) cc_final: 0.6770 (pt0) REVERT: A 318 LYS cc_start: 0.7166 (mppt) cc_final: 0.6934 (mptt) REVERT: A 371 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8468 (tt) REVERT: A 381 ARG cc_start: 0.8012 (tpt170) cc_final: 0.7747 (tmm160) REVERT: A 474 ILE cc_start: 0.9346 (mt) cc_final: 0.9135 (mm) REVERT: A 581 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7052 (mm-30) REVERT: A 688 HIS cc_start: 0.4886 (OUTLIER) cc_final: 0.4549 (t-90) REVERT: A 705 MET cc_start: 0.8499 (mmp) cc_final: 0.8280 (mmp) REVERT: A 961 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6868 (mp0) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.1617 time to fit residues: 27.1560 Evaluate side-chains 116 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR 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 851 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.172471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.146000 restraints weight = 10115.812| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.65 r_work: 0.3680 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7319 Z= 0.113 Angle : 0.570 8.833 9898 Z= 0.286 Chirality : 0.039 0.147 1130 Planarity : 0.004 0.047 1248 Dihedral : 5.339 96.479 957 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.08 % Allowed : 16.73 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 894 helix: 1.55 (0.24), residues: 485 sheet: -1.20 (0.53), residues: 108 loop : -0.39 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.004 0.001 HIS A 155 PHE 0.026 0.002 PHE A 107 TYR 0.010 0.001 TYR A 124 ARG 0.002 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 366) hydrogen bonds : angle 4.25725 ( 1089) covalent geometry : bond 0.00258 ( 7319) covalent geometry : angle 0.57038 ( 9898) ********************** 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 116 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.887 Fit side-chains REVERT: A 125 GLU cc_start: 0.6977 (pt0) cc_final: 0.6683 (pt0) REVERT: A 284 MET cc_start: 0.1870 (ttt) cc_final: 0.0686 (tmm) REVERT: A 318 LYS cc_start: 0.7129 (mppt) cc_final: 0.6915 (mptt) REVERT: A 371 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8702 (tt) REVERT: A 474 ILE cc_start: 0.9308 (mt) cc_final: 0.9094 (mm) REVERT: A 581 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7130 (mm-30) REVERT: A 961 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6872 (mp0) outliers start: 17 outliers final: 15 residues processed: 111 average time/residue: 0.1659 time to fit residues: 26.4063 Evaluate side-chains 108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 228 LEU 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 534 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 591 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 0.0270 chunk 46 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 2 optimal weight: 0.0170 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.176458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148336 restraints weight = 9833.568| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.59 r_work: 0.3721 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3178 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= 0.097 Angle : 0.567 7.765 9898 Z= 0.279 Chirality : 0.038 0.181 1130 Planarity : 0.004 0.048 1248 Dihedral : 4.806 80.310 957 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.71 % Allowed : 17.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 894 helix: 1.61 (0.24), residues: 490 sheet: -1.22 (0.50), residues: 111 loop : -0.21 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.003 0.000 HIS A 155 PHE 0.018 0.001 PHE A 325 TYR 0.008 0.001 TYR A 288 ARG 0.002 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 366) hydrogen bonds : angle 4.19115 ( 1089) covalent geometry : bond 0.00209 ( 7319) covalent geometry : angle 0.56741 ( 9898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.50 seconds wall clock time: 54 minutes 36.03 seconds (3276.03 seconds total)