Starting phenix.real_space_refine on Tue Feb 11 09:06:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w4s_21539/02_2025/6w4s_21539.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w4s_21539/02_2025/6w4s_21539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w4s_21539/02_2025/6w4s_21539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w4s_21539/02_2025/6w4s_21539.map" model { file = "/net/cci-nas-00/data/ceres_data/6w4s_21539/02_2025/6w4s_21539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w4s_21539/02_2025/6w4s_21539.cif" } resolution = 3.2 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= -0.041 sd= 0.719 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 29 5.16 5 C 3240 2.51 5 N 814 2.21 5 O 903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4986 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3216 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 412} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.37, per 1000 atoms: 0.68 Number of scatterers: 4986 At special positions: 0 Unit cell: (100.158, 98.4608, 92.5192, 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 29 16.00 O 903 8.00 N 814 7.00 C 3240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 633.7 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 8 sheets defined 60.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 25 through 55 Processing helix chain 'F' and resid 57 through 86 removed outlier: 5.183A pdb=" N ALA F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN F 86 " --> pdb=" O TRP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 116 removed outlier: 3.649A pdb=" N ILE F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 125 through 157 removed outlier: 4.326A pdb=" N LEU F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.507A pdb=" N VAL F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 198 removed outlier: 4.236A pdb=" N LEU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 186 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Proline residue: F 189 - end of helix Processing helix chain 'F' and resid 200 through 230 removed outlier: 3.694A pdb=" N GLY F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER F 209 " --> pdb=" O CYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 234 removed outlier: 3.622A pdb=" N ALA F 234 " --> pdb=" O PRO F 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 231 through 234' Processing helix chain 'F' and resid 292 through 304 removed outlier: 3.694A pdb=" N ASN F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.560A pdb=" N LEU F 317 " --> pdb=" O GLY F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 338 through 367 Processing helix chain 'F' and resid 370 through 393 removed outlier: 3.903A pdb=" N LEU F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL F 391 " --> pdb=" O CYS F 387 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE F 392 " --> pdb=" O VAL F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 484 removed outlier: 4.547A pdb=" N ILE F 467 " --> pdb=" O ILE F 463 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 514 Processing helix chain 'F' and resid 516 through 546 removed outlier: 4.133A pdb=" N LEU F 525 " --> pdb=" O GLY F 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.863A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.628A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.389A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.772A pdb=" N CYS L 23 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.736A pdb=" N VAL L 13 " --> pdb=" O GLU L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR L 101 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1539 1.34 - 1.46: 1053 1.46 - 1.58: 2463 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5101 Sorted by residual: bond pdb=" CA ASP L 86 " pdb=" C ASP L 86 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.80e-02 3.09e+03 1.86e+00 bond pdb=" CG1 ILE H 37 " pdb=" CD1 ILE H 37 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.70e-01 bond pdb=" N VAL L 62 " pdb=" CA VAL L 62 " ideal model delta sigma weight residual 1.468 1.460 0.009 1.05e-02 9.07e+03 6.89e-01 bond pdb=" CB ASP F 473 " pdb=" CG ASP F 473 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.26e-01 bond pdb=" CB ASN L 95 " pdb=" CG ASN L 95 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 ... (remaining 5096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 6615 1.16 - 2.33: 276 2.33 - 3.49: 45 3.49 - 4.66: 12 4.66 - 5.82: 4 Bond angle restraints: 6952 Sorted by residual: angle pdb=" N ILE F 186 " pdb=" CA ILE F 186 " pdb=" C ILE F 186 " ideal model delta sigma weight residual 113.42 110.12 3.30 1.17e+00 7.31e-01 7.93e+00 angle pdb=" C GLY F 55 " pdb=" N ASN F 56 " pdb=" CA ASN F 56 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" C PHE F 472 " pdb=" N ASP F 473 " pdb=" CA ASP F 473 " ideal model delta sigma weight residual 120.31 116.82 3.49 1.52e+00 4.33e-01 5.28e+00 angle pdb=" N PRO L 50 " pdb=" CA PRO L 50 " pdb=" C PRO L 50 " ideal model delta sigma weight residual 110.21 113.76 -3.55 1.64e+00 3.72e-01 4.68e+00 angle pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 ... (remaining 6947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 2640 16.75 - 33.50: 250 33.50 - 50.25: 46 50.25 - 66.99: 16 66.99 - 83.74: 5 Dihedral angle restraints: 2957 sinusoidal: 1085 harmonic: 1872 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 136.54 -43.54 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA LEU L 54 " pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 475 0.027 - 0.053: 211 0.053 - 0.080: 89 0.080 - 0.107: 37 0.107 - 0.133: 12 Chirality restraints: 824 Sorted by residual: chirality pdb=" CA ILE L 52 " pdb=" N ILE L 52 " pdb=" C ILE L 52 " pdb=" CB ILE L 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ASN F 56 " pdb=" N ASN F 56 " pdb=" C ASN F 56 " pdb=" CB ASN F 56 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 821 not shown) Planarity restraints: 849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 516 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO F 517 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 517 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 517 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 47 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO L 48 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 48 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 48 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 40 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO H 41 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.019 5.00e-02 4.00e+02 ... (remaining 846 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 5211 3.27 - 3.81: 7917 3.81 - 4.36: 9283 4.36 - 4.90: 16708 Nonbonded interactions: 39386 Sorted by model distance: nonbonded pdb=" OG1 THR F 122 " pdb=" O ARG L 96 " model vdw 2.176 3.040 nonbonded pdb=" NE2 GLN L 93 " pdb=" OD1 ASN L 95 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASN H 60 " pdb=" OG SER H 62 " model vdw 2.240 3.040 nonbonded pdb=" O VAL F 67 " pdb=" OG SER F 71 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU F 119 " pdb=" OH TYR H 33 " model vdw 2.260 3.040 ... (remaining 39381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.470 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5101 Z= 0.276 Angle : 0.571 5.823 6952 Z= 0.331 Chirality : 0.039 0.133 824 Planarity : 0.004 0.049 849 Dihedral : 14.378 83.741 1757 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.45 % Allowed : 11.87 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.13 (0.33), residues: 640 helix: 0.50 (0.27), residues: 371 sheet: -0.84 (0.53), residues: 100 loop : -3.49 (0.37), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 470 HIS 0.004 0.001 HIS F 507 PHE 0.018 0.001 PHE F 295 TYR 0.019 0.002 TYR H 78 ARG 0.002 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.512 Fit side-chains REVERT: F 42 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.8337 (t-100) REVERT: F 112 MET cc_start: 0.7755 (mmm) cc_final: 0.7532 (mmm) REVERT: F 167 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (mmt-90) REVERT: F 385 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8752 (tt) REVERT: F 482 GLU cc_start: 0.7658 (tt0) cc_final: 0.7205 (tt0) REVERT: F 486 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7573 (tm-30) REVERT: F 540 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6696 (ttt90) REVERT: L 24 ARG cc_start: 0.7906 (mpp-170) cc_final: 0.7693 (ptt90) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.1642 time to fit residues: 26.4574 Evaluate side-chains 111 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 TRP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 527 SER Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN F 99 GLN F 141 ASN F 174 ASN F 185 ASN F 481 GLN F 496 GLN F 516 ASN H 16 GLN H 35 ASN H 76 ASN H 77 HIS L 38 HIS L 78 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104669 restraints weight = 7750.204| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.79 r_work: 0.3198 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5101 Z= 0.206 Angle : 0.541 6.267 6952 Z= 0.297 Chirality : 0.040 0.205 824 Planarity : 0.004 0.040 849 Dihedral : 7.010 58.523 731 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.27 % Allowed : 16.88 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.56 (0.35), residues: 640 helix: 1.81 (0.28), residues: 370 sheet: -0.03 (0.55), residues: 102 loop : -2.76 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 470 HIS 0.003 0.001 HIS F 507 PHE 0.012 0.001 PHE F 295 TYR 0.017 0.002 TYR H 78 ARG 0.002 0.000 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.555 Fit side-chains REVERT: F 385 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8551 (tt) REVERT: F 474 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7482 (mp) REVERT: F 540 ARG cc_start: 0.6862 (mtm180) cc_final: 0.6358 (ttm-80) REVERT: L 24 ARG cc_start: 0.8127 (mpp-170) cc_final: 0.7257 (ptt90) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.1777 time to fit residues: 26.8460 Evaluate side-chains 106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109842 restraints weight = 7666.141| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.74 r_work: 0.3239 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5101 Z= 0.163 Angle : 0.516 6.130 6952 Z= 0.278 Chirality : 0.039 0.136 824 Planarity : 0.004 0.040 849 Dihedral : 5.797 54.437 711 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.64 % Allowed : 17.63 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.24 (0.35), residues: 640 helix: 2.32 (0.28), residues: 369 sheet: 0.08 (0.56), residues: 100 loop : -2.20 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.003 0.001 HIS L 94 PHE 0.011 0.001 PHE F 295 TYR 0.016 0.001 TYR H 78 ARG 0.003 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: F 166 ASP cc_start: 0.8179 (t0) cc_final: 0.7965 (t0) REVERT: F 385 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8433 (tt) REVERT: F 386 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7605 (tt) REVERT: F 540 ARG cc_start: 0.6845 (mtm180) cc_final: 0.6357 (ttm-80) REVERT: L 24 ARG cc_start: 0.8078 (mpp-170) cc_final: 0.7269 (ptt90) REVERT: L 37 MET cc_start: 0.7922 (tpt) cc_final: 0.7608 (tpt) outliers start: 25 outliers final: 17 residues processed: 121 average time/residue: 0.1567 time to fit residues: 24.8738 Evaluate side-chains 108 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107039 restraints weight = 7806.746| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.78 r_work: 0.3198 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5101 Z= 0.260 Angle : 0.558 7.742 6952 Z= 0.298 Chirality : 0.040 0.187 824 Planarity : 0.004 0.040 849 Dihedral : 5.856 52.272 708 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.64 % Allowed : 19.67 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.24 (0.35), residues: 640 helix: 2.23 (0.28), residues: 370 sheet: 0.15 (0.56), residues: 100 loop : -2.05 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 42 HIS 0.005 0.001 HIS F 507 PHE 0.015 0.001 PHE F 295 TYR 0.019 0.002 TYR H 78 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.540 Fit side-chains REVERT: F 385 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8437 (tt) REVERT: F 386 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7611 (tt) REVERT: F 540 ARG cc_start: 0.6889 (mtm180) cc_final: 0.6312 (ttm-80) REVERT: L 17 GLN cc_start: 0.7867 (tt0) cc_final: 0.7041 (tt0) REVERT: L 24 ARG cc_start: 0.8111 (mpp-170) cc_final: 0.7318 (ptt90) outliers start: 25 outliers final: 19 residues processed: 113 average time/residue: 0.1680 time to fit residues: 24.4156 Evaluate side-chains 109 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 24 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111697 restraints weight = 7654.104| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.77 r_work: 0.3263 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5101 Z= 0.146 Angle : 0.505 6.220 6952 Z= 0.270 Chirality : 0.038 0.139 824 Planarity : 0.004 0.041 849 Dihedral : 5.350 58.821 706 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.53 % Allowed : 20.22 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.65 (0.35), residues: 640 helix: 2.47 (0.28), residues: 376 sheet: -0.02 (0.54), residues: 104 loop : -1.55 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 42 HIS 0.002 0.001 HIS L 94 PHE 0.010 0.001 PHE F 295 TYR 0.014 0.001 TYR H 78 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: F 312 MET cc_start: 0.8560 (mmm) cc_final: 0.8174 (mmm) REVERT: F 385 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (tt) REVERT: F 540 ARG cc_start: 0.6827 (mtm180) cc_final: 0.6310 (ttm-80) REVERT: H 100 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9061 (mp) REVERT: L 17 GLN cc_start: 0.7824 (tt0) cc_final: 0.7491 (tt0) REVERT: L 24 ARG cc_start: 0.7980 (mpp-170) cc_final: 0.7159 (ptt90) REVERT: L 37 MET cc_start: 0.7876 (tpt) cc_final: 0.7645 (tpt) REVERT: L 80 HIS cc_start: 0.6966 (t70) cc_final: 0.6628 (t70) REVERT: L 93 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8824 (tm-30) outliers start: 19 outliers final: 15 residues processed: 119 average time/residue: 0.1720 time to fit residues: 26.4407 Evaluate side-chains 113 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.109652 restraints weight = 7811.447| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.76 r_work: 0.3257 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5101 Z= 0.249 Angle : 0.555 6.609 6952 Z= 0.296 Chirality : 0.040 0.150 824 Planarity : 0.004 0.039 849 Dihedral : 5.440 56.316 706 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.01 % Allowed : 20.04 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.52 (0.35), residues: 640 helix: 2.31 (0.28), residues: 375 sheet: 0.18 (0.55), residues: 100 loop : -1.61 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 42 HIS 0.005 0.001 HIS F 507 PHE 0.015 0.001 PHE F 295 TYR 0.020 0.002 TYR F 133 ARG 0.002 0.000 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: F 474 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7673 (mp) REVERT: F 540 ARG cc_start: 0.6869 (mtm180) cc_final: 0.6345 (ttm-80) REVERT: L 17 GLN cc_start: 0.7809 (tt0) cc_final: 0.7503 (tt0) REVERT: L 24 ARG cc_start: 0.8216 (mpp-170) cc_final: 0.7298 (ptt90) REVERT: L 80 HIS cc_start: 0.6858 (t70) cc_final: 0.6551 (t70) outliers start: 27 outliers final: 21 residues processed: 114 average time/residue: 0.2282 time to fit residues: 34.4419 Evaluate side-chains 110 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111090 restraints weight = 7608.579| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.70 r_work: 0.3279 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5101 Z= 0.193 Angle : 0.545 7.740 6952 Z= 0.289 Chirality : 0.039 0.161 824 Planarity : 0.004 0.039 849 Dihedral : 4.921 51.731 704 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.01 % Allowed : 20.04 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.61 (0.35), residues: 640 helix: 2.34 (0.28), residues: 375 sheet: 0.23 (0.55), residues: 100 loop : -1.47 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.003 0.001 HIS L 94 PHE 0.012 0.001 PHE F 295 TYR 0.017 0.002 TYR F 220 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: F 474 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7675 (mp) REVERT: F 540 ARG cc_start: 0.6829 (mtm180) cc_final: 0.6299 (ttm-80) REVERT: H 100 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9112 (mp) REVERT: L 17 GLN cc_start: 0.7779 (tt0) cc_final: 0.7488 (tt0) REVERT: L 24 ARG cc_start: 0.8182 (mpp-170) cc_final: 0.7281 (ptt90) REVERT: L 37 MET cc_start: 0.7942 (tpt) cc_final: 0.7565 (tpt) REVERT: L 80 HIS cc_start: 0.6799 (t70) cc_final: 0.6539 (t70) outliers start: 27 outliers final: 23 residues processed: 114 average time/residue: 0.1657 time to fit residues: 24.4583 Evaluate side-chains 114 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112031 restraints weight = 7700.835| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.72 r_work: 0.3289 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5101 Z= 0.177 Angle : 0.535 7.234 6952 Z= 0.285 Chirality : 0.039 0.153 824 Planarity : 0.004 0.039 849 Dihedral : 4.842 51.382 704 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.01 % Allowed : 20.96 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.68 (0.35), residues: 640 helix: 2.36 (0.28), residues: 376 sheet: 0.13 (0.54), residues: 104 loop : -1.30 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.003 0.001 HIS L 94 PHE 0.012 0.001 PHE F 295 TYR 0.021 0.002 TYR F 133 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: F 355 MET cc_start: 0.7479 (mmm) cc_final: 0.7139 (tpt) REVERT: F 385 ILE cc_start: 0.7934 (tp) cc_final: 0.7491 (pt) REVERT: F 474 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7653 (mp) REVERT: F 540 ARG cc_start: 0.6819 (mtm180) cc_final: 0.6292 (ttm-80) REVERT: L 17 GLN cc_start: 0.7785 (tt0) cc_final: 0.7496 (tt0) REVERT: L 24 ARG cc_start: 0.8177 (mpp-170) cc_final: 0.7260 (ptt90) REVERT: L 80 HIS cc_start: 0.6791 (t70) cc_final: 0.6542 (t70) REVERT: L 107 LYS cc_start: 0.8358 (tptm) cc_final: 0.8117 (tttt) outliers start: 27 outliers final: 23 residues processed: 113 average time/residue: 0.1632 time to fit residues: 23.8923 Evaluate side-chains 111 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109697 restraints weight = 7716.549| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.74 r_work: 0.3249 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5101 Z= 0.242 Angle : 0.569 7.039 6952 Z= 0.303 Chirality : 0.040 0.143 824 Planarity : 0.004 0.038 849 Dihedral : 5.011 51.012 704 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.38 % Allowed : 20.59 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.52 (0.35), residues: 640 helix: 2.19 (0.28), residues: 375 sheet: 0.43 (0.55), residues: 102 loop : -1.48 (0.48), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 42 HIS 0.004 0.001 HIS F 507 PHE 0.015 0.001 PHE F 295 TYR 0.018 0.002 TYR H 78 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: F 383 CYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7946 (t) REVERT: F 385 ILE cc_start: 0.7928 (tp) cc_final: 0.7452 (pt) REVERT: F 474 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7680 (mp) REVERT: F 486 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7716 (tm-30) REVERT: F 540 ARG cc_start: 0.6802 (mtm180) cc_final: 0.6289 (ttm-80) REVERT: L 17 GLN cc_start: 0.7815 (tt0) cc_final: 0.7152 (tt0) REVERT: L 24 ARG cc_start: 0.8222 (mpp-170) cc_final: 0.7322 (ptt90) REVERT: L 107 LYS cc_start: 0.8418 (tptm) cc_final: 0.8177 (tttt) outliers start: 29 outliers final: 24 residues processed: 113 average time/residue: 0.1739 time to fit residues: 26.0936 Evaluate side-chains 111 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 TYR Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111760 restraints weight = 7709.776| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.76 r_work: 0.3281 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5101 Z= 0.181 Angle : 0.556 8.779 6952 Z= 0.291 Chirality : 0.039 0.147 824 Planarity : 0.004 0.040 849 Dihedral : 4.865 51.737 704 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.82 % Allowed : 21.52 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.68 (0.35), residues: 640 helix: 2.34 (0.28), residues: 376 sheet: 0.07 (0.53), residues: 106 loop : -1.19 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 34 HIS 0.003 0.001 HIS F 507 PHE 0.012 0.001 PHE F 295 TYR 0.016 0.001 TYR H 78 ARG 0.002 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: F 42 TRP cc_start: 0.8544 (t-100) cc_final: 0.8331 (t-100) REVERT: F 355 MET cc_start: 0.7452 (mmm) cc_final: 0.7136 (tpt) REVERT: F 383 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7764 (t) REVERT: F 385 ILE cc_start: 0.7864 (tp) cc_final: 0.7376 (pt) REVERT: F 474 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7610 (mp) REVERT: F 486 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7636 (tm-30) REVERT: F 540 ARG cc_start: 0.6823 (mtm180) cc_final: 0.6315 (ttt90) REVERT: L 17 GLN cc_start: 0.7767 (tt0) cc_final: 0.7486 (tt0) REVERT: L 24 ARG cc_start: 0.8140 (mpp-170) cc_final: 0.7235 (ptt90) REVERT: L 80 HIS cc_start: 0.6870 (t70) cc_final: 0.6567 (t70) REVERT: L 107 LYS cc_start: 0.8362 (tptm) cc_final: 0.8135 (tttt) REVERT: L 111 LYS cc_start: 0.6432 (mtmt) cc_final: 0.6220 (mtmm) outliers start: 26 outliers final: 23 residues processed: 111 average time/residue: 0.1747 time to fit residues: 25.2877 Evaluate side-chains 114 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 TYR Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 0.0370 chunk 32 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113815 restraints weight = 7611.973| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.75 r_work: 0.3365 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5101 Z= 0.164 Angle : 0.555 9.180 6952 Z= 0.289 Chirality : 0.040 0.243 824 Planarity : 0.004 0.040 849 Dihedral : 4.688 50.114 704 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.45 % Allowed : 22.08 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.79 (0.35), residues: 640 helix: 2.41 (0.28), residues: 376 sheet: 0.11 (0.52), residues: 106 loop : -1.10 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 42 HIS 0.003 0.001 HIS F 507 PHE 0.011 0.001 PHE F 295 TYR 0.015 0.001 TYR F 220 ARG 0.007 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.11 seconds wall clock time: 46 minutes 15.96 seconds (2775.96 seconds total)