Starting phenix.real_space_refine on Fri Dec 27 09:33:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xon_33353/12_2024/7xon_33353.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xon_33353/12_2024/7xon_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_33353/12_2024/7xon_33353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xon_33353/12_2024/7xon_33353.map" model { file = "/net/cci-nas-00/data/ceres_data/7xon_33353/12_2024/7xon_33353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xon_33353/12_2024/7xon_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-5532/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: 3.22, 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: 1.05 Conformation dependent library (CDL) restraints added in 454.9 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: 0.37 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: 0.97 Time building geometry restraints manager: 1.21 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: 1.130 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- 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 : 0.512 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: 0.1829 time to fit residues: 8.7684 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 : 0.487 ------------------------------------------------------------------------------- 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: 9.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 : 0.356 Fit side-chains REVERT: B 52 ASP cc_start: 0.8331 (t70) cc_final: 0.8082 (t0) REVERT: B 193 MET cc_start: 0.8780 (ttm) cc_final: 0.8413 (ttm) REVERT: B 307 MET cc_start: 0.8548 (mpp) cc_final: 0.8230 (mpp) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.0932 time to fit residues: 3.8382 Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 39 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.0570 chunk 42 optimal weight: 0.0870 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.8282 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3883 Z= 0.191 Angle : 0.449 5.823 5243 Z= 0.243 Chirality : 0.040 0.133 638 Planarity : 0.002 0.018 687 Dihedral : 3.657 17.839 552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.50 % Allowed : 8.91 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.37), residues: 522 helix: 2.69 (0.29), residues: 299 sheet: 0.81 (0.58), residues: 80 loop : -0.16 (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 0.008 0.001 TYR B 506 ARG 0.003 0.000 ARG B 421 *********************** 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: 2 poor density : 22 time to evaluate : 0.524 Fit side-chains REVERT: B 52 ASP cc_start: 0.8343 (t70) cc_final: 0.8081 (t0) REVERT: B 193 MET cc_start: 0.8777 (ttm) cc_final: 0.8451 (ttm) REVERT: B 307 MET cc_start: 0.8551 (mpp) cc_final: 0.8254 (mpp) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.1172 time to fit residues: 4.0105 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 : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3883 Z= 0.335 Angle : 0.516 5.657 5243 Z= 0.276 Chirality : 0.042 0.140 638 Planarity : 0.003 0.020 687 Dihedral : 3.799 17.471 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.24 % Allowed : 9.90 % Favored : 88.86 % 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: 2.43 (0.36), residues: 522 helix: 2.62 (0.29), residues: 300 sheet: 0.82 (0.57), residues: 80 loop : -0.13 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.009 0.001 PHE B 219 TYR 0.012 0.001 TYR B 506 ARG 0.004 0.000 ARG B 452 *********************** 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 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.468 Fit side-chains REVERT: B 52 ASP cc_start: 0.8408 (t70) cc_final: 0.8043 (t0) REVERT: B 193 MET cc_start: 0.8816 (ttm) cc_final: 0.8462 (ttm) REVERT: B 307 MET cc_start: 0.8541 (mpp) cc_final: 0.8214 (mpp) REVERT: B 390 LYS cc_start: 0.9321 (mmtm) cc_final: 0.9114 (mmmt) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.1386 time to fit residues: 4.9528 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 : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3883 Z= 0.161 Angle : 0.447 7.035 5243 Z= 0.238 Chirality : 0.040 0.138 638 Planarity : 0.002 0.016 687 Dihedral : 3.722 18.069 552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.17 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: 2.57 (0.37), residues: 522 helix: 2.75 (0.29), residues: 299 sheet: 0.92 (0.59), residues: 80 loop : -0.14 (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 0.008 0.001 TYR B 476 ARG 0.003 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 : 0.492 Fit side-chains REVERT: B 193 MET cc_start: 0.8785 (ttm) cc_final: 0.8469 (ttm) REVERT: B 307 MET cc_start: 0.8557 (mpp) cc_final: 0.8250 (mpp) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.1623 time to fit residues: 5.8891 Evaluate side-chains 22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 12 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3883 Z= 0.230 Angle : 0.475 7.892 5243 Z= 0.252 Chirality : 0.040 0.132 638 Planarity : 0.002 0.016 687 Dihedral : 3.732 17.631 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.49 % Allowed : 11.39 % 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: 2.58 (0.37), residues: 522 helix: 2.74 (0.29), residues: 299 sheet: 0.98 (0.59), residues: 80 loop : -0.11 (0.50), 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 0.009 0.001 TYR B 506 ARG 0.002 0.000 ARG B 368 *********************** 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 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.484 Fit side-chains REVERT: B 193 MET cc_start: 0.8808 (ttm) cc_final: 0.8497 (ttm) REVERT: B 307 MET cc_start: 0.8549 (mpp) cc_final: 0.8242 (mpp) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.1132 time to fit residues: 4.5152 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 28 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3883 Z= 0.298 Angle : 0.507 8.670 5243 Z= 0.269 Chirality : 0.041 0.136 638 Planarity : 0.002 0.018 687 Dihedral : 3.818 17.530 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.49 % Allowed : 11.39 % 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: 2.49 (0.37), residues: 522 helix: 2.66 (0.29), residues: 300 sheet: 0.95 (0.60), residues: 80 loop : -0.15 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.008 0.001 PHE B 219 TYR 0.010 0.001 TYR B 506 ARG 0.003 0.000 ARG B 452 *********************** 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 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.507 Fit side-chains REVERT: B 193 MET cc_start: 0.8825 (ttm) cc_final: 0.8506 (ttm) REVERT: B 307 MET cc_start: 0.8513 (mpp) cc_final: 0.8178 (mpp) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.1092 time to fit residues: 4.3345 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 300 VAL 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 24 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2276 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 : 0.489 9.211 5243 Z= 0.259 Chirality : 0.040 0.133 638 Planarity : 0.002 0.014 687 Dihedral : 3.826 17.854 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.49 % Allowed : 11.39 % 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: 2.46 (0.36), residues: 522 helix: 2.65 (0.29), residues: 300 sheet: 0.95 (0.60), residues: 80 loop : -0.22 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.006 0.001 PHE B 195 TYR 0.009 0.001 TYR B 506 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 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.484 Fit side-chains REVERT: B 193 MET cc_start: 0.8810 (ttm) cc_final: 0.8497 (ttm) REVERT: B 307 MET cc_start: 0.8508 (mpp) cc_final: 0.8136 (mpp) outliers start: 6 outliers final: 6 residues processed: 26 average time/residue: 0.1180 time to fit residues: 4.6976 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 300 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 448 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2185 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= 0.127 Angle : 0.445 8.763 5243 Z= 0.238 Chirality : 0.039 0.128 638 Planarity : 0.002 0.016 687 Dihedral : 3.777 18.068 552 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.49 % Allowed : 11.88 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.37), residues: 522 helix: 2.80 (0.29), residues: 292 sheet: 1.01 (0.60), residues: 80 loop : -0.27 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.004 0.001 PHE B 195 TYR 0.008 0.001 TYR B 476 ARG 0.002 0.000 ARG B 368 *********************** 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: 6 poor density : 20 time to evaluate : 0.514 Fit side-chains REVERT: B 6 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8771 (t) REVERT: B 16 MET cc_start: 0.9148 (mtm) cc_final: 0.8860 (mtm) REVERT: B 193 MET cc_start: 0.8760 (ttm) cc_final: 0.8486 (ttm) REVERT: B 307 MET cc_start: 0.8544 (mpp) cc_final: 0.8213 (mpp) outliers start: 6 outliers final: 3 residues processed: 26 average time/residue: 0.1422 time to fit residues: 5.3045 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 : 0.530 ------------------------------------------------------------------------------- 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 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3883 Z= 0.294 Angle : 0.508 10.403 5243 Z= 0.266 Chirality : 0.040 0.135 638 Planarity : 0.002 0.020 687 Dihedral : 3.840 17.649 552 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 : 0.99 % 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: 2.45 (0.36), residues: 522 helix: 2.72 (0.29), residues: 294 sheet: 0.90 (0.60), residues: 80 loop : -0.25 (0.48), residues: 148 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 0.009 0.001 TYR B 199 ARG 0.003 0.000 ARG B 452 ********************** 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 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.472 Fit side-chains REVERT: B 193 MET cc_start: 0.8812 (ttm) cc_final: 0.8516 (ttm) REVERT: B 307 MET cc_start: 0.8503 (mpp) cc_final: 0.8152 (mpp) outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.1136 time to fit residues: 4.1810 Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.061144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.047240 restraints weight = 12775.410| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.39 r_work: 0.2725 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3883 Z= 0.380 Angle : 0.551 9.675 5243 Z= 0.290 Chirality : 0.041 0.139 638 Planarity : 0.003 0.018 687 Dihedral : 3.991 17.738 552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 2.27 (0.36), residues: 522 helix: 2.52 (0.29), residues: 300 sheet: 0.85 (0.60), residues: 80 loop : -0.33 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.008 0.002 PHE B 219 TYR 0.010 0.001 TYR B 199 ARG 0.003 0.000 ARG B 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1018.23 seconds wall clock time: 20 minutes 5.68 seconds (1205.68 seconds total)