Starting phenix.real_space_refine on Wed Mar 5 19:19:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws2_32741/03_2025/7ws2_32741.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws2_32741/03_2025/7ws2_32741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2025/7ws2_32741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2025/7ws2_32741.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2025/7ws2_32741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws2_32741/03_2025/7ws2_32741.cif" } resolution = 3.3 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= -0.003 sd= 0.025 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 15 5.16 5 C 2120 2.51 5 N 558 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1578 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 4.70, per 1000 atoms: 1.41 Number of scatterers: 3343 At special positions: 0 Unit cell: (91.84, 55.76, 95.94, 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 15 16.00 O 650 8.00 N 558 7.00 C 2120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 395.5 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 12.3% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.596A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.534A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.741A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.922A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.111A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.893A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR E 112 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 94 " --> pdb=" O THR E 117 " (cutoff:3.500A) 105 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.92 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: 1071 1.34 - 1.46: 843 1.46 - 1.58: 1496 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3428 Sorted by residual: bond pdb=" N ASP E 31 " pdb=" CA ASP E 31 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.25e-02 6.40e+03 7.53e+00 bond pdb=" N GLN D 6 " pdb=" CA GLN D 6 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.17e+00 bond pdb=" N ASN A 450 " pdb=" CA ASN A 450 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.02e+00 bond pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.32e-02 5.74e+03 6.85e+00 bond pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.26e-02 6.30e+03 6.34e+00 ... (remaining 3423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 4347 1.13 - 2.27: 240 2.27 - 3.40: 56 3.40 - 4.54: 11 4.54 - 5.67: 6 Bond angle restraints: 4660 Sorted by residual: angle pdb=" CA LEU E 105 " pdb=" C LEU E 105 " pdb=" O LEU E 105 " ideal model delta sigma weight residual 122.13 118.28 3.85 1.13e+00 7.83e-01 1.16e+01 angle pdb=" CA ASN A 501 " pdb=" C ASN A 501 " pdb=" O ASN A 501 " ideal model delta sigma weight residual 121.87 118.39 3.48 1.16e+00 7.43e-01 9.02e+00 angle pdb=" N LYS D 39 " pdb=" CA LYS D 39 " pdb=" C LYS D 39 " ideal model delta sigma weight residual 109.50 105.76 3.74 1.47e+00 4.63e-01 6.47e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 113.61 109.90 3.71 1.50e+00 4.44e-01 6.12e+00 angle pdb=" CA GLU E 103 " pdb=" C GLU E 103 " pdb=" O GLU E 103 " ideal model delta sigma weight residual 121.78 118.63 3.15 1.28e+00 6.10e-01 6.04e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1795 15.53 - 31.07: 170 31.07 - 46.60: 45 46.60 - 62.13: 7 62.13 - 77.67: 4 Dihedral angle restraints: 2021 sinusoidal: 775 harmonic: 1246 Sorted by residual: dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.73 35.73 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 122.28 -29.28 1 1.00e+01 1.00e-02 1.23e+01 ... (remaining 2018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 297 0.031 - 0.062: 135 0.062 - 0.092: 33 0.092 - 0.123: 25 0.123 - 0.154: 9 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA LYS D 39 " pdb=" N LYS D 39 " pdb=" C LYS D 39 " pdb=" CB LYS D 39 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR D 94 " pdb=" N THR D 94 " pdb=" C THR D 94 " pdb=" CB THR D 94 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA LYS A 444 " pdb=" N LYS A 444 " pdb=" C LYS A 444 " pdb=" CB LYS A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 496 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 479 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 527 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 384 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.028 5.00e-02 4.00e+02 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 747 2.79 - 3.32: 2829 3.32 - 3.84: 5241 3.84 - 4.37: 6298 4.37 - 4.90: 11020 Nonbonded interactions: 26135 Sorted by model distance: nonbonded pdb=" NH1 ARG D 61 " pdb=" OD2 ASP D 82 " model vdw 2.258 3.120 nonbonded pdb=" OH TYR D 97 " pdb=" O ILE E 104 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.269 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.292 3.040 nonbonded pdb=" O SER A 530 " pdb=" OG SER A 530 " model vdw 2.302 3.040 ... (remaining 26130 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: 0.010 Normalize map: mean=0, sd=1: 12.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.090 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3428 Z= 0.229 Angle : 0.636 5.672 4660 Z= 0.375 Chirality : 0.045 0.154 499 Planarity : 0.005 0.052 606 Dihedral : 13.310 77.666 1213 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.40), residues: 425 helix: -4.57 (0.37), residues: 33 sheet: -0.50 (0.44), residues: 158 loop : -1.21 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 53 HIS 0.001 0.000 HIS E 35 PHE 0.009 0.001 PHE D 83 TYR 0.007 0.001 TYR A 495 ARG 0.004 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.352 Fit side-chains REVERT: D 54 LEU cc_start: 0.8957 (tt) cc_final: 0.8657 (tp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2446 time to fit residues: 26.5745 Evaluate side-chains 82 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122918 restraints weight = 5276.076| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.99 r_work: 0.3441 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3428 Z= 0.314 Angle : 0.648 5.585 4660 Z= 0.347 Chirality : 0.048 0.157 499 Planarity : 0.006 0.051 606 Dihedral : 5.047 27.722 475 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.37 % Allowed : 9.62 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.39), residues: 425 helix: -3.50 (0.66), residues: 27 sheet: -0.52 (0.43), residues: 152 loop : -1.33 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.015 0.002 PHE A 490 TYR 0.019 0.002 TYR A 489 ARG 0.003 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.389 Fit side-chains REVERT: A 418 ILE cc_start: 0.9401 (mt) cc_final: 0.9196 (mt) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.1470 time to fit residues: 16.7620 Evaluate side-chains 90 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122331 restraints weight = 5274.682| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.03 r_work: 0.3432 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3428 Z= 0.254 Angle : 0.601 5.902 4660 Z= 0.317 Chirality : 0.046 0.153 499 Planarity : 0.005 0.054 606 Dihedral : 4.947 26.467 475 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.75 % Allowed : 12.09 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.39), residues: 425 helix: -3.19 (0.77), residues: 27 sheet: -0.60 (0.43), residues: 153 loop : -1.36 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE A 490 TYR 0.021 0.002 TYR E 80 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.360 Fit side-chains REVERT: A 418 ILE cc_start: 0.9413 (mt) cc_final: 0.9209 (mt) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.1666 time to fit residues: 18.1619 Evaluate side-chains 87 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.0170 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123385 restraints weight = 5267.125| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.98 r_work: 0.3451 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3428 Z= 0.229 Angle : 0.592 7.391 4660 Z= 0.306 Chirality : 0.045 0.146 499 Planarity : 0.005 0.051 606 Dihedral : 4.849 24.979 475 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.75 % Allowed : 15.66 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.39), residues: 425 helix: -3.11 (0.79), residues: 27 sheet: -0.50 (0.42), residues: 152 loop : -1.24 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE A 490 TYR 0.022 0.002 TYR E 80 ARG 0.005 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.388 Fit side-chains REVERT: A 418 ILE cc_start: 0.9402 (mt) cc_final: 0.9179 (mt) outliers start: 10 outliers final: 5 residues processed: 92 average time/residue: 0.1679 time to fit residues: 18.5348 Evaluate side-chains 90 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122824 restraints weight = 5254.677| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.98 r_work: 0.3442 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3428 Z= 0.259 Angle : 0.616 6.696 4660 Z= 0.318 Chirality : 0.046 0.163 499 Planarity : 0.005 0.050 606 Dihedral : 5.072 29.511 475 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.47 % Allowed : 17.03 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.40), residues: 425 helix: -3.03 (0.81), residues: 27 sheet: -0.50 (0.41), residues: 160 loop : -1.31 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS E 35 PHE 0.013 0.001 PHE A 490 TYR 0.018 0.002 TYR E 80 ARG 0.003 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.375 Fit side-chains REVERT: A 418 ILE cc_start: 0.9403 (mt) cc_final: 0.9176 (mt) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.2061 time to fit residues: 21.7656 Evaluate side-chains 88 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0030 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 overall best weight: 0.3668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123402 restraints weight = 5371.884| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.09 r_work: 0.3449 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3428 Z= 0.199 Angle : 0.589 6.545 4660 Z= 0.297 Chirality : 0.045 0.176 499 Planarity : 0.004 0.048 606 Dihedral : 4.832 27.416 475 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.20 % Allowed : 18.68 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.40), residues: 425 helix: -3.00 (0.82), residues: 27 sheet: -0.45 (0.41), residues: 161 loop : -1.24 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE A 490 TYR 0.017 0.001 TYR D 92 ARG 0.006 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.486 Fit side-chains REVERT: A 418 ILE cc_start: 0.9399 (mt) cc_final: 0.9157 (mt) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.1672 time to fit residues: 17.6737 Evaluate side-chains 86 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123371 restraints weight = 5224.333| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.90 r_work: 0.3452 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3428 Z= 0.294 Angle : 0.646 8.506 4660 Z= 0.328 Chirality : 0.046 0.166 499 Planarity : 0.005 0.051 606 Dihedral : 5.136 27.786 475 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.67 % Allowed : 16.76 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.40), residues: 425 helix: -3.18 (0.76), residues: 27 sheet: -0.45 (0.42), residues: 160 loop : -1.34 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.002 PHE A 490 TYR 0.018 0.002 TYR D 92 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.637 Fit side-chains REVERT: D 106 GLU cc_start: 0.7660 (tp30) cc_final: 0.7420 (tp30) REVERT: A 418 ILE cc_start: 0.9383 (mt) cc_final: 0.9157 (mt) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.2070 time to fit residues: 23.1039 Evaluate side-chains 91 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122738 restraints weight = 5226.887| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.89 r_work: 0.3448 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3428 Z= 0.309 Angle : 0.657 8.479 4660 Z= 0.335 Chirality : 0.047 0.187 499 Planarity : 0.005 0.055 606 Dihedral : 5.277 27.163 475 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.12 % Allowed : 18.41 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.40), residues: 425 helix: -3.27 (0.74), residues: 27 sheet: -0.29 (0.42), residues: 155 loop : -1.42 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.002 PHE A 490 TYR 0.017 0.002 TYR D 92 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.389 Fit side-chains REVERT: D 106 GLU cc_start: 0.7656 (tp30) cc_final: 0.7397 (tp30) REVERT: A 418 ILE cc_start: 0.9384 (mt) cc_final: 0.9164 (mt) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1667 time to fit residues: 17.4918 Evaluate side-chains 90 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 104 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124231 restraints weight = 5230.360| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.92 r_work: 0.3476 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3428 Z= 0.230 Angle : 0.621 8.718 4660 Z= 0.312 Chirality : 0.045 0.170 499 Planarity : 0.005 0.054 606 Dihedral : 5.047 26.690 475 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.12 % Allowed : 18.13 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.40), residues: 425 helix: -3.25 (0.76), residues: 27 sheet: -0.38 (0.41), residues: 161 loop : -1.35 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.012 0.001 PHE A 490 TYR 0.016 0.001 TYR D 92 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.392 Fit side-chains REVERT: D 106 GLU cc_start: 0.7544 (tp30) cc_final: 0.7293 (tp30) REVERT: A 418 ILE cc_start: 0.9385 (mt) cc_final: 0.9152 (mt) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.1562 time to fit residues: 17.2079 Evaluate side-chains 87 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124010 restraints weight = 5167.051| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.91 r_work: 0.3464 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3428 Z= 0.268 Angle : 0.633 7.040 4660 Z= 0.325 Chirality : 0.046 0.170 499 Planarity : 0.005 0.055 606 Dihedral : 5.141 26.052 475 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.02 % Allowed : 18.41 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.40), residues: 425 helix: -3.20 (0.79), residues: 27 sheet: -0.38 (0.41), residues: 161 loop : -1.36 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 490 TYR 0.018 0.002 TYR D 92 ARG 0.002 0.000 ARG E 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.363 Fit side-chains REVERT: D 106 GLU cc_start: 0.7586 (tp30) cc_final: 0.7338 (tp30) REVERT: A 418 ILE cc_start: 0.9383 (mt) cc_final: 0.9160 (mt) REVERT: E 39 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7768 (tp-100) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.1560 time to fit residues: 16.0513 Evaluate side-chains 87 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 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 = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122217 restraints weight = 5223.067| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.89 r_work: 0.3440 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3428 Z= 0.357 Angle : 0.675 7.169 4660 Z= 0.353 Chirality : 0.048 0.185 499 Planarity : 0.005 0.057 606 Dihedral : 5.430 26.541 475 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.75 % Allowed : 18.13 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.39), residues: 425 helix: -3.19 (0.79), residues: 27 sheet: -0.31 (0.41), residues: 157 loop : -1.44 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.004 0.002 HIS E 35 PHE 0.018 0.002 PHE A 490 TYR 0.020 0.002 TYR D 92 ARG 0.002 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.07 seconds wall clock time: 45 minutes 27.47 seconds (2727.47 seconds total)