Starting phenix.real_space_refine on Wed Mar 5 22:34:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xon_33353/03_2025/7xon_33353.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xon_33353/03_2025/7xon_33353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xon_33353/03_2025/7xon_33353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xon_33353/03_2025/7xon_33353.map" model { file = "/net/cci-nas-00/data/ceres_data/7xon_33353/03_2025/7xon_33353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xon_33353/03_2025/7xon_33353.cif" } resolution = 3.1 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= 0.006 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 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 3.23, per 1000 atoms: 0.84 Number of scatterers: 3855 At special positions: 0 Unit cell: (71.34, 74.82, 85.26, 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 20 16.00 O 773 8.00 N 665 7.00 C 2397 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: 0.87 Conformation dependent library (CDL) restraints added in 485.8 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 59.9% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.509A pdb=" N ARG B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.781A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 110 removed outlier: 3.562A pdb=" N ALA B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 169 removed outlier: 3.700A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 243 Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.689A pdb=" N ALA B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.914A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.623A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 459 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.591A pdb=" N ALA B 251 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'B' and resid 476 through 479 267 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.03 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: 1341 1.34 - 1.46: 643 1.46 - 1.58: 1862 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CB LYS B 242 " pdb=" CG LYS B 242 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.25e-01 bond pdb=" CG LYS B 242 " pdb=" CD LYS B 242 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.97e-01 bond pdb=" CA ALA B 449 " pdb=" C ALA B 449 " ideal model delta sigma weight residual 1.520 1.529 -0.008 1.23e-02 6.61e+03 4.72e-01 bond pdb=" CB LYS B 142 " pdb=" CG LYS B 142 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.06e-01 bond pdb=" CA GLU B 61 " pdb=" C GLU B 61 " ideal model delta sigma weight residual 1.523 1.529 -0.007 1.10e-02 8.26e+03 3.56e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 5117 1.20 - 2.41: 88 2.41 - 3.61: 32 3.61 - 4.82: 3 4.82 - 6.02: 3 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N GLY B 9 " pdb=" CA GLY B 9 " pdb=" C GLY B 9 " ideal model delta sigma weight residual 111.24 116.45 -5.21 1.49e+00 4.50e-01 1.22e+01 angle pdb=" N ILE B 230 " pdb=" CA ILE B 230 " pdb=" C ILE B 230 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CB LYS B 242 " pdb=" CG LYS B 242 " pdb=" CD LYS B 242 " ideal model delta sigma weight residual 111.30 117.32 -6.02 2.30e+00 1.89e-01 6.85e+00 angle pdb=" CA LYS B 142 " pdb=" CB LYS B 142 " pdb=" CG LYS B 142 " ideal model delta sigma weight residual 114.10 118.66 -4.56 2.00e+00 2.50e-01 5.20e+00 angle pdb=" CA ILE B 230 " pdb=" C ILE B 230 " pdb=" N ARG B 231 " ideal model delta sigma weight residual 118.65 116.61 2.04 1.07e+00 8.73e-01 3.62e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 2240 17.17 - 34.34: 136 34.34 - 51.51: 25 51.51 - 68.68: 5 68.68 - 85.85: 6 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA MET B 166 " pdb=" C MET B 166 " pdb=" N ASP B 167 " pdb=" CA ASP B 167 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " pdb=" OD1 ASP B 428 " ideal model delta sinusoidal sigma weight residual -30.00 -85.61 55.61 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA LYS B 245 " pdb=" CB LYS B 245 " pdb=" CG LYS B 245 " pdb=" CD LYS B 245 " ideal model delta sinusoidal sigma weight residual -180.00 -126.14 -53.86 3 1.50e+01 4.44e-03 9.24e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 370 0.024 - 0.047: 143 0.047 - 0.071: 66 0.071 - 0.095: 33 0.095 - 0.118: 26 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL B 213 " pdb=" N VAL B 213 " pdb=" C VAL B 213 " pdb=" CB VAL B 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE B 332 " pdb=" N ILE B 332 " pdb=" C ILE B 332 " pdb=" CB ILE B 332 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 245 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.15e-01 pdb=" N PRO B 246 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 461 " 0.013 5.00e-02 4.00e+02 1.92e-02 5.88e-01 pdb=" N PRO B 462 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 46 " -0.010 5.00e-02 4.00e+02 1.57e-02 3.96e-01 pdb=" N PRO B 47 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO B 47 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO B 47 " -0.009 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1202 2.84 - 3.35: 4019 3.35 - 3.87: 6388 3.87 - 4.38: 6838 4.38 - 4.90: 12153 Nonbonded interactions: 30600 Sorted by model distance: nonbonded pdb=" NH1 ARG B 421 " pdb=" O VAL B 469 " model vdw 2.325 3.120 nonbonded pdb=" O GLU B 339 " pdb=" NE2 GLN B 343 " model vdw 2.333 3.120 nonbonded pdb=" O SER B 463 " pdb=" ND2 ASN B 467 " model vdw 2.363 3.120 nonbonded pdb=" OD1 ASN B 229 " pdb=" N ILE B 230 " model vdw 2.377 3.120 nonbonded pdb=" NH2 ARG B 421 " pdb=" O TYR B 476 " model vdw 2.386 3.120 ... (remaining 30595 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 0.027 3883 Z= 0.145 Angle : 0.467 6.021 5243 Z= 0.257 Chirality : 0.039 0.118 638 Planarity : 0.002 0.023 687 Dihedral : 12.444 85.845 1464 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 2.61 (0.37), residues: 522 helix: 2.76 (0.30), residues: 290 sheet: 0.99 (0.61), residues: 74 loop : 0.16 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.007 0.001 PHE B 195 TYR 0.007 0.001 TYR B 199 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 52 ASP cc_start: 0.8163 (t70) cc_final: 0.7961 (t0) REVERT: B 73 MET cc_start: 0.8729 (ptp) cc_final: 0.8454 (ptm) REVERT: B 121 ASP cc_start: 0.8773 (m-30) cc_final: 0.8464 (m-30) REVERT: B 254 VAL cc_start: 0.9521 (t) cc_final: 0.9133 (t) REVERT: B 307 MET cc_start: 0.8529 (mpp) cc_final: 0.8222 (mpp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1722 time to fit residues: 8.2613 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.063598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049724 restraints weight = 12899.745| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.40 r_work: 0.2797 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3883 Z= 0.282 Angle : 0.519 5.192 5243 Z= 0.279 Chirality : 0.042 0.142 638 Planarity : 0.003 0.019 687 Dihedral : 3.679 17.361 552 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.74 % Allowed : 6.19 % Favored : 93.07 % 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: 2.49 (0.36), residues: 522 helix: 2.67 (0.29), residues: 299 sheet: 0.90 (0.59), residues: 74 loop : -0.09 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.006 0.001 PHE B 66 TYR 0.007 0.001 TYR B 506 ARG 0.005 0.001 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.397 Fit side-chains REVERT: B 193 MET cc_start: 0.9160 (ttm) cc_final: 0.8901 (ttm) REVERT: B 307 MET cc_start: 0.8711 (mpp) cc_final: 0.8363 (mpp) REVERT: B 338 GLU cc_start: 0.8468 (tp30) cc_final: 0.8235 (tp30) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.1077 time to fit residues: 4.3777 Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 330 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.062026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048404 restraints weight = 12922.700| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.42 r_work: 0.2762 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3883 Z= 0.258 Angle : 0.478 5.060 5243 Z= 0.258 Chirality : 0.041 0.136 638 Planarity : 0.002 0.016 687 Dihedral : 3.702 17.751 552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.74 % Allowed : 8.42 % Favored : 90.84 % 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: 2.45 (0.36), residues: 522 helix: 2.64 (0.29), residues: 300 sheet: 0.93 (0.59), residues: 74 loop : -0.15 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.006 0.001 PHE B 219 TYR 0.009 0.001 TYR B 506 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: B 193 MET cc_start: 0.9201 (ttm) cc_final: 0.8982 (ttm) REVERT: B 307 MET cc_start: 0.8730 (mpp) cc_final: 0.8384 (mpp) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1203 time to fit residues: 4.0238 Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.062318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048622 restraints weight = 12922.990| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.49 r_work: 0.2766 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3883 Z= 0.200 Angle : 0.448 5.895 5243 Z= 0.241 Chirality : 0.040 0.132 638 Planarity : 0.002 0.016 687 Dihedral : 3.667 17.819 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.74 % Allowed : 9.90 % Favored : 89.36 % 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: 2.52 (0.36), residues: 522 helix: 2.71 (0.29), residues: 299 sheet: 0.94 (0.59), residues: 74 loop : -0.11 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.005 0.001 PHE B 219 TYR 0.009 0.001 TYR B 506 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 193 MET cc_start: 0.9176 (ttm) cc_final: 0.8967 (ttm) REVERT: B 307 MET cc_start: 0.8715 (mpp) cc_final: 0.8379 (mpp) outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 0.1245 time to fit residues: 4.3651 Evaluate side-chains 22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.062384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048664 restraints weight = 13152.116| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.48 r_work: 0.2763 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3883 Z= 0.193 Angle : 0.456 7.251 5243 Z= 0.241 Chirality : 0.040 0.131 638 Planarity : 0.002 0.017 687 Dihedral : 3.673 17.804 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.74 % Allowed : 11.39 % Favored : 87.87 % 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: 2.55 (0.37), residues: 522 helix: 2.74 (0.29), residues: 299 sheet: 0.85 (0.59), residues: 80 loop : -0.10 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.006 0.001 PHE B 195 TYR 0.008 0.001 TYR B 506 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8717 (mpp) cc_final: 0.8389 (mpp) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.1544 time to fit residues: 5.5231 Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.061379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.047822 restraints weight = 12989.201| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.45 r_work: 0.2742 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3883 Z= 0.270 Angle : 0.499 7.892 5243 Z= 0.263 Chirality : 0.040 0.134 638 Planarity : 0.002 0.017 687 Dihedral : 3.728 17.527 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.49 % Allowed : 11.63 % Favored : 86.88 % 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: 2.55 (0.37), residues: 522 helix: 2.69 (0.29), residues: 299 sheet: 1.07 (0.61), residues: 74 loop : -0.07 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.008 0.001 PHE B 195 TYR 0.009 0.001 TYR B 506 ARG 0.003 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8708 (mpp) cc_final: 0.8380 (mpp) outliers start: 6 outliers final: 5 residues processed: 27 average time/residue: 0.1080 time to fit residues: 4.4515 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.062463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048839 restraints weight = 12958.268| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.49 r_work: 0.2775 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3883 Z= 0.149 Angle : 0.450 8.861 5243 Z= 0.236 Chirality : 0.039 0.127 638 Planarity : 0.002 0.016 687 Dihedral : 3.663 17.854 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.49 % Allowed : 11.63 % Favored : 86.88 % 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: 2.61 (0.37), residues: 522 helix: 2.77 (0.29), residues: 299 sheet: 0.97 (0.60), residues: 80 loop : -0.08 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.005 0.001 PHE B 195 TYR 0.007 0.001 TYR B 199 ARG 0.002 0.000 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8687 (mpp) cc_final: 0.8365 (mpp) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.1207 time to fit residues: 4.8890 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.0470 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.063048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049277 restraints weight = 12866.306| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.49 r_work: 0.2788 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3883 Z= 0.129 Angle : 0.443 9.871 5243 Z= 0.233 Chirality : 0.039 0.126 638 Planarity : 0.002 0.016 687 Dihedral : 3.648 17.627 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.99 % Allowed : 12.13 % Favored : 86.88 % 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: 2.58 (0.37), residues: 522 helix: 2.75 (0.29), residues: 298 sheet: 0.78 (0.60), residues: 82 loop : -0.01 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.005 0.001 PHE B 195 TYR 0.008 0.001 TYR B 476 ARG 0.002 0.000 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8705 (mpp) cc_final: 0.8367 (mpp) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.1333 time to fit residues: 5.2350 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.061297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.047379 restraints weight = 13106.084| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.50 r_work: 0.2728 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3883 Z= 0.275 Angle : 0.520 10.025 5243 Z= 0.269 Chirality : 0.040 0.134 638 Planarity : 0.002 0.022 687 Dihedral : 3.729 17.137 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.24 % Allowed : 11.88 % Favored : 86.88 % 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: 2.52 (0.36), residues: 522 helix: 2.65 (0.29), residues: 299 sheet: 1.08 (0.62), residues: 74 loop : -0.06 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.008 0.001 PHE B 195 TYR 0.011 0.001 TYR B 506 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8728 (mpp) cc_final: 0.8369 (mpp) outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.1084 time to fit residues: 4.3014 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.063986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049948 restraints weight = 12725.481| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.42 r_work: 0.2805 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3883 Z= 0.149 Angle : 0.472 9.502 5243 Z= 0.246 Chirality : 0.039 0.127 638 Planarity : 0.002 0.016 687 Dihedral : 3.676 17.756 552 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.99 % Allowed : 11.88 % Favored : 87.13 % 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: 2.48 (0.37), residues: 522 helix: 2.64 (0.29), residues: 299 sheet: 0.94 (0.60), residues: 80 loop : -0.10 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.005 0.001 PHE B 195 TYR 0.007 0.001 TYR B 199 ARG 0.002 0.000 ARG B 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: B 16 MET cc_start: 0.9470 (mtm) cc_final: 0.9225 (mtm) REVERT: B 307 MET cc_start: 0.8696 (mpp) cc_final: 0.8316 (mpp) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.1118 time to fit residues: 4.2663 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 overall best weight: 1.1420 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.064365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050650 restraints weight = 12560.215| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.40 r_work: 0.2829 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3883 Z= 0.134 Angle : 0.456 9.226 5243 Z= 0.236 Chirality : 0.039 0.126 638 Planarity : 0.002 0.017 687 Dihedral : 3.622 17.614 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.24 % Allowed : 11.39 % Favored : 87.38 % 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: 2.48 (0.37), residues: 522 helix: 2.69 (0.29), residues: 298 sheet: 0.77 (0.60), residues: 82 loop : -0.09 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.005 0.001 PHE B 195 TYR 0.007 0.001 TYR B 506 ARG 0.002 0.000 ARG B 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.80 seconds wall clock time: 33 minutes 52.85 seconds (2032.85 seconds total)