Starting phenix.real_space_refine on Thu Jun 5 07:28:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r1y_14243/06_2025/7r1y_14243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1y_14243/06_2025/7r1y_14243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r1y_14243/06_2025/7r1y_14243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1y_14243/06_2025/7r1y_14243.map" model { file = "/net/cci-nas-00/data/ceres_data/7r1y_14243/06_2025/7r1y_14243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1y_14243/06_2025/7r1y_14243.cif" } resolution = 3.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3615 2.51 5 N 982 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 5704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5704 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 689} Chain breaks: 11 Time building chain proxies: 3.71, per 1000 atoms: 0.65 Number of scatterers: 5704 At special positions: 0 Unit cell: (71.9488, 74.752, 122.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1074 8.00 N 982 7.00 C 3615 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: 1.28 Conformation dependent library (CDL) restraints added in 799.8 milliseconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 43.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 19 through 37 removed outlier: 3.679A pdb=" N ARG A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.633A pdb=" N GLN A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.522A pdb=" N VAL A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 326 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.781A pdb=" N SER A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 529 through 542 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 647 through 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 689 through 710 Processing helix chain 'A' and resid 761 through 787 Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 797 through 806 removed outlier: 3.605A pdb=" N ILE A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 818 through 834 removed outlier: 3.534A pdb=" N ASP A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 854 through 870 Processing helix chain 'A' and resid 875 through 892 removed outlier: 3.620A pdb=" N LYS A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 881 " --> pdb=" O THR A 877 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.516A pdb=" N VAL A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 927 removed outlier: 3.589A pdb=" N ASP A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.552A pdb=" N CYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.797A pdb=" N TYR A 355 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 376 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 353 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.546A pdb=" N ALA A 446 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.584A pdb=" N GLY A 107 " --> pdb=" O TRP A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 220 removed outlier: 6.627A pdb=" N ALA A 229 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 218 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A 227 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 226 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 271 removed outlier: 3.694A pdb=" N GLN A 267 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 287 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 286 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 303 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 288 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 400 removed outlier: 3.707A pdb=" N ARG A 396 " --> pdb=" O ALA A 407 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 801 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: 2.07 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1895 1.34 - 1.46: 1156 1.46 - 1.58: 2701 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5801 Sorted by residual: bond pdb=" C PRO A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.23e+00 bond pdb=" C VAL A 897 " pdb=" N ASP A 898 " ideal model delta sigma weight residual 1.328 1.340 -0.012 1.30e-02 5.92e+03 9.08e-01 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.29e-01 bond pdb=" C ALA A 229 " pdb=" N GLY A 230 " ideal model delta sigma weight residual 1.331 1.319 0.012 1.46e-02 4.69e+03 6.71e-01 bond pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 1.517 1.524 -0.007 9.30e-03 1.16e+04 6.23e-01 ... (remaining 5796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 7744 1.80 - 3.60: 96 3.60 - 5.40: 9 5.40 - 7.19: 2 7.19 - 8.99: 1 Bond angle restraints: 7852 Sorted by residual: angle pdb=" N ILE A 893 " pdb=" CA ILE A 893 " pdb=" C ILE A 893 " ideal model delta sigma weight residual 113.20 109.80 3.40 9.60e-01 1.09e+00 1.25e+01 angle pdb=" C VAL A 897 " pdb=" N ASP A 898 " pdb=" CA ASP A 898 " ideal model delta sigma weight residual 122.82 127.52 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" C SER A 83 " pdb=" N ILE A 84 " pdb=" CA ILE A 84 " ideal model delta sigma weight residual 122.93 119.05 3.88 1.21e+00 6.83e-01 1.03e+01 angle pdb=" N ASP A 898 " pdb=" CA ASP A 898 " pdb=" C ASP A 898 " ideal model delta sigma weight residual 111.17 115.52 -4.35 1.41e+00 5.03e-01 9.51e+00 angle pdb=" N PRO A 110 " pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 110.70 114.00 -3.30 1.22e+00 6.72e-01 7.33e+00 ... (remaining 7847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3267 17.24 - 34.47: 189 34.47 - 51.71: 80 51.71 - 68.94: 8 68.94 - 86.18: 4 Dihedral angle restraints: 3548 sinusoidal: 1438 harmonic: 2110 Sorted by residual: dihedral pdb=" CA HIS A 349 " pdb=" C HIS A 349 " pdb=" N ALA A 350 " pdb=" CA ALA A 350 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PRO A 468 " pdb=" C PRO A 468 " pdb=" N ILE A 469 " pdb=" CA ILE A 469 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ILE A 469 " pdb=" C ILE A 469 " pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 539 0.027 - 0.054: 225 0.054 - 0.081: 86 0.081 - 0.108: 37 0.108 - 0.135: 24 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CG LEU A 228 " pdb=" CB LEU A 228 " pdb=" CD1 LEU A 228 " pdb=" CD2 LEU A 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 416 " pdb=" N ILE A 416 " pdb=" C ILE A 416 " pdb=" CB ILE A 416 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 908 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 52 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 110 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 111 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 473 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.022 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1103 2.78 - 3.31: 5462 3.31 - 3.84: 9467 3.84 - 4.37: 11138 4.37 - 4.90: 19024 Nonbonded interactions: 46194 Sorted by model distance: nonbonded pdb=" N LEU A 145 " pdb=" O ALA A 168 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR A 169 " pdb=" O ASP A 172 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLN A 287 " pdb=" OH TYR A 289 " model vdw 2.334 3.040 nonbonded pdb=" OE1 GLN A 891 " pdb=" OG1 THR A 921 " model vdw 2.353 3.040 nonbonded pdb=" OD2 ASP A 232 " pdb=" OH TYR A 236 " model vdw 2.361 3.040 ... (remaining 46189 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.440 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:34.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.002 0.039 5801 Z= 0.115 Angle : 0.524 8.992 7852 Z= 0.293 Chirality : 0.041 0.135 911 Planarity : 0.004 0.046 1008 Dihedral : 13.126 86.178 2170 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.44 % Allowed : 11.42 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.32), residues: 699 helix: 1.36 (0.31), residues: 286 sheet: -0.03 (0.42), residues: 156 loop : -0.79 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.014 0.001 PHE A 497 TYR 0.007 0.001 TYR A 206 ARG 0.003 0.000 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.12620 ( 283) hydrogen bonds : angle 5.25988 ( 801) covalent geometry : bond 0.00236 ( 5801) covalent geometry : angle 0.52371 ( 7852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.661 Fit side-chains REVERT: A 157 PHE cc_start: 0.3986 (OUTLIER) cc_final: 0.3626 (t80) REVERT: A 806 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7312 (tt) REVERT: A 855 THR cc_start: 0.7815 (p) cc_final: 0.7476 (t) REVERT: A 962 THR cc_start: 0.6266 (m) cc_final: 0.5905 (p) outliers start: 22 outliers final: 8 residues processed: 128 average time/residue: 1.1297 time to fit residues: 152.8198 Evaluate side-chains 71 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 891 GLN ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.172316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150757 restraints weight = 8998.348| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.88 r_work: 0.3901 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5801 Z= 0.136 Angle : 0.583 9.456 7852 Z= 0.300 Chirality : 0.042 0.164 911 Planarity : 0.005 0.040 1008 Dihedral : 6.292 52.111 787 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.48 % Allowed : 16.43 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.78 (0.32), residues: 699 helix: 1.88 (0.31), residues: 283 sheet: 0.06 (0.43), residues: 148 loop : -0.66 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.013 0.001 PHE A 497 TYR 0.013 0.001 TYR A 128 ARG 0.006 0.001 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 283) hydrogen bonds : angle 4.26939 ( 801) covalent geometry : bond 0.00310 ( 5801) covalent geometry : angle 0.58312 ( 7852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.723 Fit side-chains REVERT: A 39 MET cc_start: 0.6228 (ptt) cc_final: 0.6002 (pmt) REVERT: A 157 PHE cc_start: 0.4116 (OUTLIER) cc_final: 0.3684 (t80) REVERT: A 691 GLN cc_start: 0.7377 (tp40) cc_final: 0.7079 (tp40) REVERT: A 780 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6460 (tt) REVERT: A 806 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7285 (tt) REVERT: A 855 THR cc_start: 0.7900 (p) cc_final: 0.7615 (t) REVERT: A 911 PHE cc_start: 0.7231 (t80) cc_final: 0.6945 (t80) REVERT: A 962 THR cc_start: 0.6272 (m) cc_final: 0.5899 (p) outliers start: 35 outliers final: 15 residues processed: 98 average time/residue: 0.9805 time to fit residues: 102.6304 Evaluate side-chains 76 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 897 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.0020 chunk 11 optimal weight: 0.9980 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN A 864 ASN A 868 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.171814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.149834 restraints weight = 9120.627| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.91 r_work: 0.3892 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5801 Z= 0.134 Angle : 0.563 8.571 7852 Z= 0.288 Chirality : 0.042 0.186 911 Planarity : 0.004 0.039 1008 Dihedral : 6.013 52.343 784 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.42 % Allowed : 16.59 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.32), residues: 699 helix: 1.91 (0.31), residues: 287 sheet: 0.05 (0.43), residues: 148 loop : -0.68 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.020 0.002 TYR A 775 ARG 0.003 0.000 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 283) hydrogen bonds : angle 4.18454 ( 801) covalent geometry : bond 0.00308 ( 5801) covalent geometry : angle 0.56256 ( 7852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.655 Fit side-chains REVERT: A 105 MET cc_start: 0.7443 (mtt) cc_final: 0.7131 (mtp) REVERT: A 157 PHE cc_start: 0.4153 (OUTLIER) cc_final: 0.3677 (t80) REVERT: A 691 GLN cc_start: 0.7392 (tp40) cc_final: 0.7141 (tp40) REVERT: A 780 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6582 (tt) REVERT: A 806 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7296 (tt) REVERT: A 855 THR cc_start: 0.7921 (p) cc_final: 0.7657 (t) REVERT: A 912 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.4285 (p90) REVERT: A 962 THR cc_start: 0.6266 (m) cc_final: 0.5949 (p) outliers start: 41 outliers final: 17 residues processed: 99 average time/residue: 0.8579 time to fit residues: 90.7267 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.0050 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.172416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150505 restraints weight = 9168.519| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.88 r_work: 0.3897 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5801 Z= 0.128 Angle : 0.567 11.455 7852 Z= 0.288 Chirality : 0.043 0.199 911 Planarity : 0.004 0.039 1008 Dihedral : 5.761 51.772 782 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.63 % Allowed : 18.15 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.86 (0.32), residues: 699 helix: 1.92 (0.31), residues: 287 sheet: 0.10 (0.43), residues: 148 loop : -0.61 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 124 TYR 0.021 0.001 TYR A 775 ARG 0.003 0.000 ARG A 501 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 283) hydrogen bonds : angle 4.14228 ( 801) covalent geometry : bond 0.00292 ( 5801) covalent geometry : angle 0.56707 ( 7852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.553 Fit side-chains REVERT: A 25 ASN cc_start: 0.6289 (t0) cc_final: 0.6046 (m-40) REVERT: A 105 MET cc_start: 0.7359 (mtt) cc_final: 0.7120 (mtm) REVERT: A 136 TYR cc_start: 0.4916 (OUTLIER) cc_final: 0.4566 (p90) REVERT: A 157 PHE cc_start: 0.4262 (OUTLIER) cc_final: 0.3684 (t80) REVERT: A 780 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6486 (tt) REVERT: A 855 THR cc_start: 0.7898 (p) cc_final: 0.7649 (t) REVERT: A 912 TYR cc_start: 0.5077 (OUTLIER) cc_final: 0.4395 (p90) REVERT: A 962 THR cc_start: 0.6216 (m) cc_final: 0.5892 (p) outliers start: 36 outliers final: 17 residues processed: 94 average time/residue: 0.8304 time to fit residues: 83.2681 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.171906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.150252 restraints weight = 8981.534| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.88 r_work: 0.3889 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5801 Z= 0.126 Angle : 0.555 7.554 7852 Z= 0.288 Chirality : 0.042 0.180 911 Planarity : 0.004 0.039 1008 Dihedral : 5.406 52.082 778 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.95 % Allowed : 19.41 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.95 (0.32), residues: 699 helix: 2.01 (0.31), residues: 287 sheet: 0.11 (0.44), residues: 148 loop : -0.56 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.005 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.020 0.001 TYR A 775 ARG 0.002 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 283) hydrogen bonds : angle 4.05881 ( 801) covalent geometry : bond 0.00287 ( 5801) covalent geometry : angle 0.55535 ( 7852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 0.600 Fit side-chains REVERT: A 25 ASN cc_start: 0.6325 (t0) cc_final: 0.6079 (m-40) REVERT: A 105 MET cc_start: 0.7492 (mtt) cc_final: 0.7197 (mtm) REVERT: A 136 TYR cc_start: 0.4930 (OUTLIER) cc_final: 0.4580 (p90) REVERT: A 157 PHE cc_start: 0.4147 (OUTLIER) cc_final: 0.3635 (t80) REVERT: A 691 GLN cc_start: 0.7480 (tp40) cc_final: 0.7217 (tp40) REVERT: A 775 TYR cc_start: 0.7633 (t80) cc_final: 0.7417 (t80) REVERT: A 780 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6476 (tt) REVERT: A 855 THR cc_start: 0.7923 (p) cc_final: 0.7630 (t) REVERT: A 895 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.6175 (m-40) REVERT: A 912 TYR cc_start: 0.5036 (OUTLIER) cc_final: 0.4746 (p90) REVERT: A 962 THR cc_start: 0.6204 (m) cc_final: 0.5877 (p) REVERT: A 966 GLN cc_start: 0.6950 (mt0) cc_final: 0.6427 (mm-40) outliers start: 38 outliers final: 19 residues processed: 92 average time/residue: 0.9136 time to fit residues: 89.2114 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.173360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.151562 restraints weight = 8952.704| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.88 r_work: 0.3906 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5801 Z= 0.116 Angle : 0.550 7.575 7852 Z= 0.284 Chirality : 0.042 0.203 911 Planarity : 0.004 0.040 1008 Dihedral : 5.305 51.078 778 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.48 % Allowed : 20.97 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.33), residues: 699 helix: 2.10 (0.31), residues: 287 sheet: 0.09 (0.44), residues: 149 loop : -0.48 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.020 0.001 TYR A 775 ARG 0.005 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 283) hydrogen bonds : angle 3.99811 ( 801) covalent geometry : bond 0.00263 ( 5801) covalent geometry : angle 0.55037 ( 7852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.686 Fit side-chains REVERT: A 25 ASN cc_start: 0.6274 (t0) cc_final: 0.6057 (m-40) REVERT: A 105 MET cc_start: 0.7493 (mtt) cc_final: 0.7249 (mtm) REVERT: A 157 PHE cc_start: 0.4197 (OUTLIER) cc_final: 0.3702 (t80) REVERT: A 691 GLN cc_start: 0.7453 (tp40) cc_final: 0.7222 (tp40) REVERT: A 780 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6555 (tt) REVERT: A 855 THR cc_start: 0.7847 (p) cc_final: 0.7557 (t) REVERT: A 895 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6221 (m-40) REVERT: A 912 TYR cc_start: 0.4861 (OUTLIER) cc_final: 0.4476 (p90) REVERT: A 962 THR cc_start: 0.6192 (m) cc_final: 0.5877 (p) REVERT: A 966 GLN cc_start: 0.6965 (mt0) cc_final: 0.6448 (mm-40) outliers start: 35 outliers final: 20 residues processed: 86 average time/residue: 0.8120 time to fit residues: 74.8792 Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147246 restraints weight = 9020.440| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.89 r_work: 0.3854 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5801 Z= 0.177 Angle : 0.619 10.365 7852 Z= 0.319 Chirality : 0.046 0.295 911 Planarity : 0.004 0.039 1008 Dihedral : 5.734 56.008 778 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.95 % Allowed : 20.66 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.72 (0.32), residues: 699 helix: 1.78 (0.31), residues: 286 sheet: -0.03 (0.44), residues: 148 loop : -0.61 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 116 HIS 0.006 0.001 HIS A 498 PHE 0.010 0.002 PHE A 497 TYR 0.012 0.002 TYR A 206 ARG 0.005 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 283) hydrogen bonds : angle 4.34213 ( 801) covalent geometry : bond 0.00411 ( 5801) covalent geometry : angle 0.61872 ( 7852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 61 time to evaluate : 0.679 Fit side-chains REVERT: A 25 ASN cc_start: 0.6310 (t0) cc_final: 0.6062 (m-40) REVERT: A 105 MET cc_start: 0.7493 (mtt) cc_final: 0.7162 (mtm) REVERT: A 136 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.4698 (p90) REVERT: A 232 ASP cc_start: 0.7462 (p0) cc_final: 0.7261 (p0) REVERT: A 691 GLN cc_start: 0.7471 (tp40) cc_final: 0.7224 (tp40) REVERT: A 780 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6434 (tt) REVERT: A 855 THR cc_start: 0.7926 (p) cc_final: 0.7621 (t) REVERT: A 895 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6118 (m-40) REVERT: A 962 THR cc_start: 0.6216 (m) cc_final: 0.5882 (p) outliers start: 38 outliers final: 23 residues processed: 89 average time/residue: 0.9561 time to fit residues: 90.6596 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 214 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 0.0370 chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.174734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153262 restraints weight = 8874.580| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.88 r_work: 0.3928 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5801 Z= 0.110 Angle : 0.569 10.481 7852 Z= 0.290 Chirality : 0.043 0.222 911 Planarity : 0.004 0.046 1008 Dihedral : 5.209 49.992 778 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.54 % Allowed : 22.38 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.32), residues: 699 helix: 2.09 (0.31), residues: 287 sheet: 0.04 (0.44), residues: 148 loop : -0.44 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.006 0.001 TYR A 128 ARG 0.006 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 283) hydrogen bonds : angle 4.04221 ( 801) covalent geometry : bond 0.00243 ( 5801) covalent geometry : angle 0.56897 ( 7852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.655 Fit side-chains REVERT: A 157 PHE cc_start: 0.4332 (OUTLIER) cc_final: 0.3795 (t80) REVERT: A 780 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6140 (tt) REVERT: A 855 THR cc_start: 0.7803 (p) cc_final: 0.7537 (t) REVERT: A 895 ASN cc_start: 0.6653 (OUTLIER) cc_final: 0.6152 (m-40) REVERT: A 962 THR cc_start: 0.6168 (m) cc_final: 0.5849 (p) REVERT: A 966 GLN cc_start: 0.6934 (mt0) cc_final: 0.6459 (mm-40) outliers start: 29 outliers final: 14 residues processed: 87 average time/residue: 1.3128 time to fit residues: 121.0785 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 39 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN A 905 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152970 restraints weight = 8918.885| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.87 r_work: 0.3923 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5801 Z= 0.123 Angle : 0.585 11.041 7852 Z= 0.300 Chirality : 0.044 0.234 911 Planarity : 0.004 0.043 1008 Dihedral : 4.949 48.311 776 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.29 % Allowed : 24.26 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.97 (0.32), residues: 699 helix: 1.96 (0.31), residues: 288 sheet: 0.09 (0.44), residues: 148 loop : -0.44 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.008 0.001 TYR A 775 ARG 0.006 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 283) hydrogen bonds : angle 4.01190 ( 801) covalent geometry : bond 0.00287 ( 5801) covalent geometry : angle 0.58455 ( 7852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.804 Fit side-chains REVERT: A 691 GLN cc_start: 0.7486 (tp40) cc_final: 0.7216 (tp40) REVERT: A 701 LYS cc_start: 0.7015 (tttp) cc_final: 0.6733 (mtpp) REVERT: A 771 VAL cc_start: 0.7403 (p) cc_final: 0.7185 (t) REVERT: A 780 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6213 (tt) REVERT: A 855 THR cc_start: 0.7772 (p) cc_final: 0.7490 (t) REVERT: A 895 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6187 (m-40) REVERT: A 962 THR cc_start: 0.6155 (m) cc_final: 0.5831 (p) REVERT: A 966 GLN cc_start: 0.6954 (mt0) cc_final: 0.6467 (mm-40) outliers start: 21 outliers final: 15 residues processed: 72 average time/residue: 1.0179 time to fit residues: 77.9734 Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 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 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.173327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.151459 restraints weight = 9025.205| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.90 r_work: 0.3900 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5801 Z= 0.134 Angle : 0.600 11.055 7852 Z= 0.306 Chirality : 0.044 0.228 911 Planarity : 0.004 0.044 1008 Dihedral : 5.068 49.597 776 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.44 % Allowed : 24.10 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.92 (0.32), residues: 699 helix: 1.92 (0.31), residues: 287 sheet: 0.00 (0.44), residues: 149 loop : -0.44 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.008 0.001 TYR A 775 ARG 0.006 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 283) hydrogen bonds : angle 4.06259 ( 801) covalent geometry : bond 0.00316 ( 5801) covalent geometry : angle 0.59965 ( 7852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.641 Fit side-chains REVERT: A 93 LEU cc_start: 0.6600 (mp) cc_final: 0.6385 (mt) REVERT: A 157 PHE cc_start: 0.4129 (OUTLIER) cc_final: 0.3611 (t80) REVERT: A 660 MET cc_start: 0.7450 (mmm) cc_final: 0.6871 (tpp) REVERT: A 691 GLN cc_start: 0.7389 (tp40) cc_final: 0.7163 (tp40) REVERT: A 692 LEU cc_start: 0.8007 (tp) cc_final: 0.7807 (tp) REVERT: A 780 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6301 (tt) REVERT: A 855 THR cc_start: 0.7777 (p) cc_final: 0.7501 (t) REVERT: A 895 ASN cc_start: 0.6715 (OUTLIER) cc_final: 0.6221 (m-40) REVERT: A 962 THR cc_start: 0.6155 (m) cc_final: 0.5825 (p) REVERT: A 966 GLN cc_start: 0.6985 (mt0) cc_final: 0.6482 (mm-40) outliers start: 22 outliers final: 13 residues processed: 76 average time/residue: 0.9317 time to fit residues: 75.4019 Evaluate side-chains 72 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.174143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.152628 restraints weight = 9105.891| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.88 r_work: 0.3918 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5801 Z= 0.121 Angle : 0.591 10.546 7852 Z= 0.299 Chirality : 0.043 0.220 911 Planarity : 0.004 0.044 1008 Dihedral : 4.988 49.554 776 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.66 % Allowed : 25.20 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.32), residues: 699 helix: 2.02 (0.31), residues: 287 sheet: 0.14 (0.45), residues: 146 loop : -0.40 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.009 0.001 TYR A 775 ARG 0.006 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 283) hydrogen bonds : angle 4.01156 ( 801) covalent geometry : bond 0.00280 ( 5801) covalent geometry : angle 0.59138 ( 7852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4391.68 seconds wall clock time: 77 minutes 19.19 seconds (4639.19 seconds total)