Starting phenix.real_space_refine on Mon Feb 10 23:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9js4_61766/02_2025/9js4_61766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9js4_61766/02_2025/9js4_61766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9js4_61766/02_2025/9js4_61766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9js4_61766/02_2025/9js4_61766.map" model { file = "/net/cci-nas-00/data/ceres_data/9js4_61766/02_2025/9js4_61766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9js4_61766/02_2025/9js4_61766.cif" } resolution = 3.8 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= -0.002 sd= 0.057 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 2065 2.51 5 N 544 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3244 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 854 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Chain: "C" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Time building chain proxies: 3.02, per 1000 atoms: 0.93 Number of scatterers: 3244 At special positions: 0 Unit cell: (66, 73.7, 101.2, 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 620 8.00 N 544 7.00 C 2065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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: 0.69 Conformation dependent library (CDL) restraints added in 409.9 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.6% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.588A pdb=" N ILE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.509A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 372 removed outlier: 4.562A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.619A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.957A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.905A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 4.019A pdb=" N THR A 5 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.589A pdb=" N HIS A 90 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 100 " --> pdb=" O HIS A 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.679A pdb=" N THR B 68 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.832A pdb=" N TYR B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 50 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.111A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.692A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) 59 hydrogen bonds defined for protein. 147 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: 0.75 Time building geometry restraints manager: 0.84 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: 1041 1.34 - 1.46: 861 1.46 - 1.58: 1409 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3329 Sorted by residual: bond pdb=" CA VAL B 63 " pdb=" CB VAL B 63 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.04e+00 bond pdb=" CG PRO C 384 " pdb=" CD PRO C 384 " ideal model delta sigma weight residual 1.503 1.533 -0.030 3.40e-02 8.65e+02 7.77e-01 bond pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.62e-01 bond pdb=" CB ASN A 31 " pdb=" CG ASN A 31 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.29e-01 bond pdb=" CA ASN A 31 " pdb=" CB ASN A 31 " ideal model delta sigma weight residual 1.533 1.546 -0.013 1.66e-02 3.63e+03 5.73e-01 ... (remaining 3324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 4289 1.22 - 2.44: 191 2.44 - 3.67: 41 3.67 - 4.89: 11 4.89 - 6.11: 2 Bond angle restraints: 4534 Sorted by residual: angle pdb=" CA CYS C 361 " pdb=" CB CYS C 361 " pdb=" SG CYS C 361 " ideal model delta sigma weight residual 114.40 120.51 -6.11 2.30e+00 1.89e-01 7.06e+00 angle pdb=" CA TYR A 91 " pdb=" CB TYR A 91 " pdb=" CG TYR A 91 " ideal model delta sigma weight residual 113.90 118.45 -4.55 1.80e+00 3.09e-01 6.39e+00 angle pdb=" C SER A 30 " pdb=" N ASN A 31 " pdb=" CA ASN A 31 " ideal model delta sigma weight residual 123.91 127.83 -3.92 1.66e+00 3.63e-01 5.56e+00 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 116.81 -4.47 2.04e+00 2.40e-01 4.80e+00 angle pdb=" CA ASN A 31 " pdb=" CB ASN A 31 " pdb=" CG ASN A 31 " ideal model delta sigma weight residual 112.60 114.76 -2.16 1.00e+00 1.00e+00 4.65e+00 ... (remaining 4529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 1728 14.78 - 29.56: 174 29.56 - 44.34: 51 44.34 - 59.12: 6 59.12 - 73.90: 5 Dihedral angle restraints: 1964 sinusoidal: 760 harmonic: 1204 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 163.36 -70.36 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 1961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 262 0.027 - 0.054: 129 0.054 - 0.080: 57 0.080 - 0.107: 30 0.107 - 0.134: 12 Chirality restraints: 490 Sorted by residual: chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ASN A 31 " pdb=" N ASN A 31 " pdb=" C ASN A 31 " pdb=" CB ASN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 487 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 383 " -0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO C 384 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO C 463 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 52 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO B 53 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " 0.019 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 913 2.81 - 3.33: 2664 3.33 - 3.85: 4632 3.85 - 4.38: 4990 4.38 - 4.90: 9122 Nonbonded interactions: 22321 Sorted by model distance: nonbonded pdb=" OG1 THR B 28 " pdb=" O ALA C 475 " model vdw 2.286 3.040 nonbonded pdb=" ND2 ASN A 96 " pdb=" OD2 ASP C 405 " model vdw 2.331 3.120 nonbonded pdb=" NE2 GLN A 38 " pdb=" O LYS A 39 " model vdw 2.380 3.120 nonbonded pdb=" NH1 ARG B 38 " pdb=" OD1 ASP B 89 " model vdw 2.403 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" OD2 ASP C 467 " model vdw 2.418 3.120 ... (remaining 22316 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 group one per residue 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: 2.570 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.600 Find NCS groups from input model: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3329 Z= 0.160 Angle : 0.615 6.111 4534 Z= 0.329 Chirality : 0.044 0.134 490 Planarity : 0.006 0.089 589 Dihedral : 12.564 73.350 1184 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 (0.38), residues: 409 helix: -3.08 (0.79), residues: 20 sheet: -0.42 (0.47), residues: 120 loop : -1.48 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.010 0.001 PHE B 67 TYR 0.014 0.001 TYR C 501 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.364 Fit side-chains REVERT: B 84 SER cc_start: 0.7991 (t) cc_final: 0.7750 (t) REVERT: C 405 ASP cc_start: 0.7173 (t70) cc_final: 0.6891 (t0) REVERT: C 489 TYR cc_start: 0.6868 (m-10) cc_final: 0.6433 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1121 time to fit residues: 8.5620 Evaluate side-chains 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.168514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154248 restraints weight = 6431.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156651 restraints weight = 4479.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158253 restraints weight = 3389.533| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3329 Z= 0.212 Angle : 0.634 5.102 4534 Z= 0.337 Chirality : 0.046 0.169 490 Planarity : 0.005 0.060 589 Dihedral : 5.539 27.449 461 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.54 % Allowed : 8.45 % 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: -1.91 (0.38), residues: 409 helix: -3.02 (0.82), residues: 20 sheet: -0.46 (0.48), residues: 114 loop : -1.56 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.005 0.002 HIS C 519 PHE 0.012 0.002 PHE C 400 TYR 0.016 0.002 TYR C 489 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.363 Fit side-chains REVERT: B 84 SER cc_start: 0.7993 (t) cc_final: 0.7737 (t) REVERT: B 106 MET cc_start: 0.8253 (mmt) cc_final: 0.7674 (mmt) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.1066 time to fit residues: 8.4551 Evaluate side-chains 49 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 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 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.168852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153891 restraints weight = 6416.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156487 restraints weight = 4340.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158486 restraints weight = 3231.669| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3329 Z= 0.199 Angle : 0.608 6.169 4534 Z= 0.322 Chirality : 0.046 0.165 490 Planarity : 0.005 0.050 589 Dihedral : 5.397 19.974 461 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.25 % Allowed : 11.83 % Favored : 85.92 % 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 (0.39), residues: 409 helix: -2.64 (0.94), residues: 20 sheet: -0.53 (0.48), residues: 117 loop : -1.50 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.002 HIS C 519 PHE 0.012 0.002 PHE C 429 TYR 0.014 0.002 TYR C 489 ARG 0.002 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.343 Fit side-chains REVERT: B 84 SER cc_start: 0.7963 (t) cc_final: 0.7725 (t) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1266 time to fit residues: 8.1869 Evaluate side-chains 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.169205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154034 restraints weight = 6540.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.156792 restraints weight = 4344.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158787 restraints weight = 3184.634| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3329 Z= 0.177 Angle : 0.577 5.085 4534 Z= 0.307 Chirality : 0.045 0.163 490 Planarity : 0.005 0.045 589 Dihedral : 5.296 19.415 461 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.97 % Allowed : 12.39 % Favored : 85.63 % 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: -1.83 (0.39), residues: 409 helix: -2.32 (1.05), residues: 20 sheet: -0.50 (0.50), residues: 110 loop : -1.50 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.010 0.001 PHE C 400 TYR 0.015 0.001 TYR C 489 ARG 0.001 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.361 Fit side-chains REVERT: B 84 SER cc_start: 0.7968 (t) cc_final: 0.7743 (t) REVERT: C 405 ASP cc_start: 0.7705 (t0) cc_final: 0.7451 (t0) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.1076 time to fit residues: 7.1254 Evaluate side-chains 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.167608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152317 restraints weight = 6523.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155058 restraints weight = 4385.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157059 restraints weight = 3220.223| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3329 Z= 0.212 Angle : 0.601 5.421 4534 Z= 0.320 Chirality : 0.045 0.164 490 Planarity : 0.005 0.043 589 Dihedral : 5.430 19.825 461 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.54 % Allowed : 13.24 % Favored : 84.23 % 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: -1.92 (0.39), residues: 409 helix: -2.86 (0.91), residues: 21 sheet: -0.60 (0.50), residues: 110 loop : -1.50 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.012 0.002 PHE C 429 TYR 0.014 0.002 TYR A 49 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.338 Fit side-chains REVERT: B 84 SER cc_start: 0.7969 (t) cc_final: 0.7747 (t) REVERT: C 405 ASP cc_start: 0.7638 (t0) cc_final: 0.7363 (t0) REVERT: C 489 TYR cc_start: 0.7068 (m-10) cc_final: 0.6788 (m-10) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.1043 time to fit residues: 7.4651 Evaluate side-chains 47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.167752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152630 restraints weight = 6597.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155420 restraints weight = 4374.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.157458 restraints weight = 3183.933| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3329 Z= 0.207 Angle : 0.626 6.218 4534 Z= 0.329 Chirality : 0.046 0.162 490 Planarity : 0.005 0.042 589 Dihedral : 5.415 19.527 461 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.82 % Allowed : 13.80 % Favored : 83.38 % 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: -1.96 (0.39), residues: 409 helix: -2.84 (0.92), residues: 20 sheet: -0.63 (0.50), residues: 111 loop : -1.54 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.012 0.002 PHE C 429 TYR 0.013 0.002 TYR A 49 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.355 Fit side-chains REVERT: B 84 SER cc_start: 0.7959 (t) cc_final: 0.7735 (t) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.1062 time to fit residues: 7.4616 Evaluate side-chains 49 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.169744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.155670 restraints weight = 6391.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.158258 restraints weight = 4268.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160202 restraints weight = 3130.487| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3329 Z= 0.160 Angle : 0.592 5.943 4534 Z= 0.309 Chirality : 0.044 0.160 490 Planarity : 0.004 0.042 589 Dihedral : 5.239 21.404 461 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.97 % Allowed : 15.77 % Favored : 82.25 % 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: -1.84 (0.40), residues: 409 helix: -2.73 (1.00), residues: 21 sheet: -0.60 (0.50), residues: 111 loop : -1.42 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.010 0.001 PHE C 429 TYR 0.012 0.001 TYR C 489 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.343 Fit side-chains REVERT: B 84 SER cc_start: 0.7975 (t) cc_final: 0.7737 (t) REVERT: C 386 LYS cc_start: 0.3391 (mmtt) cc_final: 0.2287 (ttpt) REVERT: C 489 TYR cc_start: 0.6980 (m-80) cc_final: 0.6539 (m-80) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.1017 time to fit residues: 6.8660 Evaluate side-chains 46 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 333 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.167711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153056 restraints weight = 6492.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155709 restraints weight = 4357.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.157680 restraints weight = 3201.761| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3329 Z= 0.217 Angle : 0.640 5.882 4534 Z= 0.340 Chirality : 0.046 0.188 490 Planarity : 0.005 0.041 589 Dihedral : 5.431 19.604 461 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.10 % Allowed : 15.21 % Favored : 81.69 % 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: -1.96 (0.40), residues: 409 helix: -3.10 (0.87), residues: 21 sheet: -0.60 (0.50), residues: 110 loop : -1.52 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.014 0.002 PHE C 429 TYR 0.014 0.002 TYR A 49 ARG 0.001 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.391 Fit side-chains REVERT: B 84 SER cc_start: 0.7931 (t) cc_final: 0.7710 (t) REVERT: C 375 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6473 (t80) REVERT: C 386 LYS cc_start: 0.3072 (mmtt) cc_final: 0.2039 (ttmt) REVERT: C 489 TYR cc_start: 0.7059 (m-80) cc_final: 0.6684 (m-80) outliers start: 11 outliers final: 10 residues processed: 49 average time/residue: 0.1040 time to fit residues: 6.9861 Evaluate side-chains 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.168364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153719 restraints weight = 6549.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156405 restraints weight = 4356.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158364 restraints weight = 3183.229| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3329 Z= 0.203 Angle : 0.641 8.108 4534 Z= 0.335 Chirality : 0.045 0.181 490 Planarity : 0.005 0.041 589 Dihedral : 5.343 19.440 461 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.82 % Allowed : 16.34 % Favored : 80.85 % 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: -1.98 (0.40), residues: 409 helix: -3.27 (0.81), residues: 21 sheet: -0.58 (0.52), residues: 105 loop : -1.53 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.014 0.001 PHE C 429 TYR 0.014 0.001 TYR A 49 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.347 Fit side-chains REVERT: B 84 SER cc_start: 0.7978 (t) cc_final: 0.7737 (t) REVERT: C 375 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6449 (t80) REVERT: C 386 LYS cc_start: 0.3241 (mmtt) cc_final: 0.2205 (ttmt) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.1047 time to fit residues: 6.8057 Evaluate side-chains 49 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.168783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154353 restraints weight = 6413.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157020 restraints weight = 4261.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158771 restraints weight = 3116.964| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3329 Z= 0.191 Angle : 0.635 8.158 4534 Z= 0.332 Chirality : 0.045 0.179 490 Planarity : 0.005 0.041 589 Dihedral : 5.336 19.184 461 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.54 % Allowed : 16.34 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.84 (0.40), residues: 409 helix: -2.92 (1.07), residues: 15 sheet: -0.46 (0.53), residues: 101 loop : -1.49 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.012 0.001 PHE C 429 TYR 0.016 0.001 TYR C 489 ARG 0.001 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.395 Fit side-chains REVERT: B 84 SER cc_start: 0.7971 (t) cc_final: 0.7732 (t) REVERT: C 375 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6376 (t80) REVERT: C 386 LYS cc_start: 0.3304 (mmtt) cc_final: 0.2225 (ttmt) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.1100 time to fit residues: 7.3229 Evaluate side-chains 48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.170174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156166 restraints weight = 6424.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158764 restraints weight = 4307.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160729 restraints weight = 3166.395| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3329 Z= 0.171 Angle : 0.612 7.726 4534 Z= 0.319 Chirality : 0.044 0.170 490 Planarity : 0.004 0.042 589 Dihedral : 5.113 18.323 461 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.82 % Allowed : 16.62 % Favored : 80.56 % 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: -1.84 (0.40), residues: 409 helix: -2.87 (1.10), residues: 15 sheet: -0.54 (0.52), residues: 105 loop : -1.47 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.011 0.001 PHE C 429 TYR 0.014 0.001 TYR C 489 ARG 0.001 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.95 seconds wall clock time: 25 minutes 28.15 seconds (1528.15 seconds total)