Starting phenix.real_space_refine on Mon Feb 10 23:48:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cuj_27001/02_2025/8cuj_27001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cuj_27001/02_2025/8cuj_27001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cuj_27001/02_2025/8cuj_27001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cuj_27001/02_2025/8cuj_27001.map" model { file = "/net/cci-nas-00/data/ceres_data/8cuj_27001/02_2025/8cuj_27001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cuj_27001/02_2025/8cuj_27001.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 21 5.16 5 C 2153 2.51 5 N 526 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.92 Number of scatterers: 3293 At special positions: 0 Unit cell: (73.272, 66.456, 79.236, 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 21 16.00 O 593 8.00 N 526 7.00 C 2153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 470.9 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 83.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 18 through 41 Processing helix chain 'A' and resid 45 through 81 removed outlier: 3.675A pdb=" N LYS A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Proline residue: A 55 - end of helix removed outlier: 3.898A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 83 through 117 Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.781A pdb=" N THR A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.728A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.824A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 272 removed outlier: 3.735A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.569A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.503A pdb=" N MET A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.660A pdb=" N GLY A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 365 Proline residue: A 360 - end of helix removed outlier: 3.824A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.672A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.527A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.911A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 436 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.605A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.567A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 245 hydrogen bonds defined for protein. 723 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: 0.89 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1033 1.34 - 1.46: 659 1.46 - 1.58: 1610 1.58 - 1.70: 0 1.70 - 1.81: 39 Bond restraints: 3341 Sorted by residual: bond pdb=" CG1 ILE A 330 " pdb=" CD1 ILE A 330 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 bond pdb=" CA PHE A 54 " pdb=" C PHE A 54 " ideal model delta sigma weight residual 1.521 1.531 -0.010 1.17e-02 7.31e+03 7.45e-01 bond pdb=" C ILE A 254 " pdb=" O ILE A 254 " ideal model delta sigma weight residual 1.237 1.248 -0.010 1.29e-02 6.01e+03 6.56e-01 bond pdb=" CA MET A 258 " pdb=" C MET A 258 " ideal model delta sigma weight residual 1.521 1.531 -0.009 1.17e-02 7.31e+03 6.55e-01 bond pdb=" N ILE A 67 " pdb=" CA ILE A 67 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.25e-02 6.40e+03 5.12e-01 ... (remaining 3336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 4472 1.71 - 3.41: 48 3.41 - 5.12: 11 5.12 - 6.82: 4 6.82 - 8.53: 1 Bond angle restraints: 4536 Sorted by residual: angle pdb=" N ILE A 67 " pdb=" CA ILE A 67 " pdb=" C ILE A 67 " ideal model delta sigma weight residual 109.34 116.03 -6.69 2.08e+00 2.31e-01 1.03e+01 angle pdb=" CA LEU A 103 " pdb=" CB LEU A 103 " pdb=" CG LEU A 103 " ideal model delta sigma weight residual 116.30 124.83 -8.53 3.50e+00 8.16e-02 5.93e+00 angle pdb=" C LEU A 328 " pdb=" N MET A 329 " pdb=" CA MET A 329 " ideal model delta sigma weight residual 121.80 117.05 4.75 2.16e+00 2.14e-01 4.84e+00 angle pdb=" CB MET A 60 " pdb=" CG MET A 60 " pdb=" SD MET A 60 " ideal model delta sigma weight residual 112.70 119.16 -6.46 3.00e+00 1.11e-01 4.64e+00 angle pdb=" CA GLU A 374 " pdb=" CB GLU A 374 " pdb=" CG GLU A 374 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.59e+00 ... (remaining 4531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 1716 15.33 - 30.65: 208 30.65 - 45.98: 67 45.98 - 61.30: 9 61.30 - 76.62: 1 Dihedral angle restraints: 2001 sinusoidal: 760 harmonic: 1241 Sorted by residual: dihedral pdb=" CA VAL A 299 " pdb=" C VAL A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " ideal model delta sinusoidal sigma weight residual -180.00 -122.23 -57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET A 255 " pdb=" CG MET A 255 " pdb=" SD MET A 255 " pdb=" CE MET A 255 " ideal model delta sinusoidal sigma weight residual 60.00 112.27 -52.27 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 342 0.025 - 0.049: 126 0.049 - 0.074: 73 0.074 - 0.098: 24 0.098 - 0.123: 10 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA LEU A 337 " pdb=" N LEU A 337 " pdb=" C LEU A 337 " pdb=" CB LEU A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB THR A 326 " pdb=" CA THR A 326 " pdb=" OG1 THR A 326 " pdb=" CG2 THR A 326 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 572 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 296 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C HIS A 296 " 0.027 2.00e-02 2.50e+03 pdb=" O HIS A 296 " -0.010 2.00e-02 2.50e+03 pdb=" N SER A 297 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 374 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" CD GLU A 374 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU A 374 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 374 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 411 " 0.021 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 412 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.018 5.00e-02 4.00e+02 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 795 2.80 - 3.33: 3329 3.33 - 3.85: 5304 3.85 - 4.38: 5710 4.38 - 4.90: 10348 Nonbonded interactions: 25486 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" O HOH A 601 " model vdw 2.276 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.380 3.040 nonbonded pdb=" ND2 ASN A 366 " pdb=" OD1 ASP A 455 " model vdw 2.386 3.120 nonbonded pdb=" O ALA A 414 " pdb=" OG1 THR A 418 " model vdw 2.396 3.040 nonbonded pdb=" OD1 ASN A 366 " pdb=" O HOH A 601 " model vdw 2.462 3.040 ... (remaining 25481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.110 Find NCS groups from input model: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.045 3341 Z= 0.165 Angle : 0.531 8.526 4536 Z= 0.278 Chirality : 0.036 0.123 575 Planarity : 0.003 0.033 555 Dihedral : 14.734 76.625 1201 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 21.61 % Favored : 78.39 % 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: 1.48 (0.40), residues: 429 helix: 1.76 (0.28), residues: 337 sheet: -0.35 (1.12), residues: 18 loop : -2.37 (0.58), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 239 TYR 0.018 0.002 TYR A 305 ARG 0.001 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.369 Fit side-chains REVERT: A 329 MET cc_start: 0.4939 (mpp) cc_final: 0.4656 (mpp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1930 time to fit residues: 10.5736 Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.0050 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.188026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138585 restraints weight = 3928.605| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.08 r_work: 0.3390 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3341 Z= 0.131 Angle : 0.458 6.042 4536 Z= 0.237 Chirality : 0.035 0.115 575 Planarity : 0.003 0.031 555 Dihedral : 3.496 18.037 455 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.05 % Allowed : 17.73 % Favored : 79.22 % 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: 429 helix: 2.06 (0.28), residues: 341 sheet: 0.40 (1.09), residues: 16 loop : -2.35 (0.59), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.011 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.383 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.1537 time to fit residues: 10.7093 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.0000 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.186049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135956 restraints weight = 3890.233| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.09 r_work: 0.3386 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3341 Z= 0.145 Angle : 0.470 8.799 4536 Z= 0.239 Chirality : 0.036 0.112 575 Planarity : 0.003 0.029 555 Dihedral : 3.479 18.112 455 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.32 % Allowed : 19.11 % Favored : 77.56 % 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: 1.99 (0.40), residues: 429 helix: 2.15 (0.28), residues: 339 sheet: 0.01 (1.07), residues: 16 loop : -2.49 (0.56), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR A 305 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.321 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 56 average time/residue: 0.1402 time to fit residues: 9.9928 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.184896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134230 restraints weight = 3931.848| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.04 r_work: 0.3400 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3341 Z= 0.157 Angle : 0.470 6.795 4536 Z= 0.242 Chirality : 0.036 0.111 575 Planarity : 0.003 0.028 555 Dihedral : 3.521 18.206 455 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.88 % Allowed : 19.11 % Favored : 77.01 % 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: 1.89 (0.40), residues: 429 helix: 2.09 (0.28), residues: 339 sheet: -0.12 (1.06), residues: 16 loop : -2.57 (0.55), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR A 305 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.365 Fit side-chains REVERT: A 472 GLN cc_start: 0.7100 (tm-30) cc_final: 0.6836 (pp30) outliers start: 14 outliers final: 13 residues processed: 53 average time/residue: 0.1377 time to fit residues: 9.3413 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133863 restraints weight = 3950.943| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.10 r_work: 0.3393 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3341 Z= 0.161 Angle : 0.485 9.220 4536 Z= 0.246 Chirality : 0.036 0.114 575 Planarity : 0.003 0.028 555 Dihedral : 3.519 18.257 455 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.88 % Allowed : 20.50 % Favored : 75.62 % 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: 429 helix: 2.07 (0.28), residues: 339 sheet: -0.20 (1.02), residues: 16 loop : -2.57 (0.56), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.011 0.001 TYR A 305 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.339 Fit side-chains REVERT: A 472 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6612 (pp30) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.1389 time to fit residues: 9.3043 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132702 restraints weight = 4049.496| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.12 r_work: 0.3378 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3341 Z= 0.177 Angle : 0.493 8.324 4536 Z= 0.253 Chirality : 0.036 0.108 575 Planarity : 0.003 0.028 555 Dihedral : 3.579 18.436 455 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.16 % Allowed : 20.22 % Favored : 75.62 % 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: 1.73 (0.40), residues: 429 helix: 1.98 (0.28), residues: 339 sheet: -0.29 (1.01), residues: 16 loop : -2.64 (0.55), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.013 0.002 TYR A 305 ARG 0.001 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.416 Fit side-chains REVERT: A 472 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6643 (pp30) outliers start: 15 outliers final: 12 residues processed: 53 average time/residue: 0.1440 time to fit residues: 9.9511 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.180994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130512 restraints weight = 3981.909| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.10 r_work: 0.3328 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3341 Z= 0.208 Angle : 0.515 7.672 4536 Z= 0.267 Chirality : 0.037 0.110 575 Planarity : 0.003 0.028 555 Dihedral : 3.718 18.746 455 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.71 % Allowed : 20.50 % Favored : 74.79 % 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: 1.45 (0.39), residues: 429 helix: 1.78 (0.27), residues: 339 sheet: -0.42 (1.01), residues: 16 loop : -2.69 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.014 0.002 PHE A 240 TYR 0.012 0.002 TYR A 305 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.337 Fit side-chains REVERT: A 472 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6558 (pp30) outliers start: 17 outliers final: 14 residues processed: 50 average time/residue: 0.1492 time to fit residues: 9.6579 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.185277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138938 restraints weight = 3926.101| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.32 r_work: 0.3391 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.002 0.025 3341 Z= 0.142 Angle : 0.488 9.973 4536 Z= 0.243 Chirality : 0.036 0.112 575 Planarity : 0.003 0.028 555 Dihedral : 3.514 18.058 455 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.05 % Allowed : 22.71 % Favored : 74.24 % 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: 1.76 (0.40), residues: 429 helix: 2.02 (0.28), residues: 339 sheet: -0.39 (1.01), residues: 16 loop : -2.68 (0.55), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.014 0.001 TYR A 373 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.356 Fit side-chains REVERT: A 472 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6689 (pp30) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1452 time to fit residues: 9.5808 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129810 restraints weight = 3988.790| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.11 r_work: 0.3324 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3341 Z= 0.233 Angle : 0.562 9.485 4536 Z= 0.284 Chirality : 0.038 0.125 575 Planarity : 0.003 0.026 555 Dihedral : 3.763 18.464 455 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.60 % Allowed : 22.16 % Favored : 74.24 % 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: 1.34 (0.40), residues: 429 helix: 1.72 (0.28), residues: 339 sheet: -0.54 (1.01), residues: 16 loop : -2.77 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.015 0.002 PHE A 240 TYR 0.015 0.002 TYR A 373 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.368 Fit side-chains REVERT: A 60 MET cc_start: 0.8673 (mmm) cc_final: 0.8284 (mmp) REVERT: A 416 LEU cc_start: 0.6002 (mt) cc_final: 0.5729 (mm) REVERT: A 472 GLN cc_start: 0.7126 (tm-30) cc_final: 0.6675 (pp30) outliers start: 13 outliers final: 12 residues processed: 50 average time/residue: 0.1312 time to fit residues: 8.4781 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.0050 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.183432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133710 restraints weight = 3892.081| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.10 r_work: 0.3395 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3341 Z= 0.167 Angle : 0.520 9.584 4536 Z= 0.260 Chirality : 0.036 0.113 575 Planarity : 0.003 0.027 555 Dihedral : 3.632 17.842 455 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 21.88 % Favored : 74.52 % 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: 1.52 (0.40), residues: 429 helix: 1.85 (0.28), residues: 339 sheet: -0.48 (1.02), residues: 16 loop : -2.77 (0.54), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 41 PHE 0.009 0.001 PHE A 240 TYR 0.014 0.001 TYR A 373 ARG 0.001 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.373 Fit side-chains REVERT: A 60 MET cc_start: 0.8629 (mmm) cc_final: 0.8411 (mmp) REVERT: A 472 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6715 (pp30) outliers start: 13 outliers final: 12 residues processed: 48 average time/residue: 0.1417 time to fit residues: 8.7065 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132396 restraints weight = 3962.337| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.10 r_work: 0.3378 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3341 Z= 0.183 Angle : 0.536 9.516 4536 Z= 0.267 Chirality : 0.037 0.116 575 Planarity : 0.003 0.027 555 Dihedral : 3.644 17.858 455 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.05 % Allowed : 22.44 % Favored : 74.52 % 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: 1.45 (0.40), residues: 429 helix: 1.81 (0.28), residues: 339 sheet: -0.49 (1.00), residues: 16 loop : -2.81 (0.53), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.014 0.002 TYR A 373 ARG 0.001 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.08 seconds wall clock time: 37 minutes 21.55 seconds (2241.55 seconds total)