Starting phenix.real_space_refine on Sun Mar 10 18:14:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xon_33353/03_2024/7xon_33353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xon_33353/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xon_33353/03_2024/7xon_33353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xon_33353/03_2024/7xon_33353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xon_33353/03_2024/7xon_33353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xon_33353/03_2024/7xon_33353.pdb" } 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 Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B ASP 490": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.58, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 1.47 Conformation dependent library (CDL) restraints added in 901.0 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: 0.41 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: 1.13 Time building geometry restraints manager: 1.62 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: 100.25 - 106.44: 72 106.44 - 112.63: 2155 112.63 - 118.81: 1076 118.81 - 125.00: 1926 125.00 - 131.19: 14 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 2.520 nonbonded pdb=" O GLU B 339 " pdb=" NE2 GLN B 343 " model vdw 2.333 2.520 nonbonded pdb=" O SER B 463 " pdb=" ND2 ASN B 467 " model vdw 2.363 2.520 nonbonded pdb=" OD1 ASN B 229 " pdb=" N ILE B 230 " model vdw 2.377 2.520 nonbonded pdb=" NH2 ARG B 421 " pdb=" O TYR B 476 " model vdw 2.386 2.520 ... (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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.650 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.120 Find NCS groups from input model: 0.100 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.473 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: 0.1740 time to fit residues: 8.3591 Evaluate side-chains 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8560 moved from start: 0.1220 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= 0.256 Angle : 0.501 5.607 5243 Z= 0.268 Chirality : 0.041 0.138 638 Planarity : 0.003 0.021 687 Dihedral : 3.691 17.455 552 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.50 % Allowed : 5.69 % Favored : 93.81 % 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: 1.03 (0.60), residues: 74 loop : -0.09 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.005 0.001 PHE B 66 TYR 0.007 0.001 TYR B 199 ARG 0.002 0.000 ARG B 362 *********************** 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 fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: B 52 ASP cc_start: 0.8316 (t70) cc_final: 0.8070 (t0) REVERT: B 193 MET cc_start: 0.8769 (ttm) cc_final: 0.8386 (ttm) REVERT: B 307 MET cc_start: 0.8502 (mpp) cc_final: 0.8156 (mpp) REVERT: B 338 GLU cc_start: 0.8011 (tp30) cc_final: 0.7793 (tp30) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.1191 time to fit residues: 4.9829 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1632 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= 0.257 Angle : 0.470 5.456 5243 Z= 0.252 Chirality : 0.040 0.137 638 Planarity : 0.002 0.021 687 Dihedral : 3.688 17.688 552 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 9.16 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.37), residues: 522 helix: 2.72 (0.29), residues: 300 sheet: 0.97 (0.59), residues: 74 loop : -0.15 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.006 0.001 PHE B 219 TYR 0.009 0.001 TYR B 506 ARG 0.003 0.000 ARG B 362 *********************** 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 27 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.484 Fit side-chains REVERT: B 52 ASP cc_start: 0.8405 (t70) cc_final: 0.8068 (t0) REVERT: B 193 MET cc_start: 0.8798 (ttm) cc_final: 0.8471 (ttm) REVERT: B 307 MET cc_start: 0.8472 (mpp) cc_final: 0.8115 (mpp) REVERT: B 338 GLU cc_start: 0.8067 (tp30) cc_final: 0.7865 (tp30) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.1165 time to fit residues: 4.3930 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 5 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3883 Z= 0.184 Angle : 0.436 6.609 5243 Z= 0.234 Chirality : 0.039 0.132 638 Planarity : 0.002 0.018 687 Dihedral : 3.658 17.848 552 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.50 % Allowed : 10.89 % Favored : 88.61 % 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: 2.66 (0.37), residues: 522 helix: 2.83 (0.29), residues: 300 sheet: 1.04 (0.59), residues: 74 loop : -0.13 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.005 0.001 PHE B 195 TYR 0.008 0.001 TYR B 506 ARG 0.001 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 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.495 Fit side-chains REVERT: B 193 MET cc_start: 0.8762 (ttm) cc_final: 0.8460 (ttm) REVERT: B 307 MET cc_start: 0.8467 (mpp) cc_final: 0.8104 (mpp) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1494 time to fit residues: 5.1211 Evaluate side-chains 21 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 37 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8569 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3883 Z= 0.227 Angle : 0.460 7.281 5243 Z= 0.246 Chirality : 0.039 0.133 638 Planarity : 0.002 0.020 687 Dihedral : 3.679 17.653 552 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.74 % Allowed : 12.87 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.37), residues: 522 helix: 2.78 (0.29), residues: 300 sheet: 0.97 (0.60), residues: 74 loop : -0.13 (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 195 TYR 0.009 0.001 TYR B 506 ARG 0.002 0.000 ARG B 452 *********************** 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 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.464 Fit side-chains REVERT: B 193 MET cc_start: 0.8778 (ttm) cc_final: 0.8464 (ttm) REVERT: B 307 MET cc_start: 0.8461 (mpp) cc_final: 0.8095 (mpp) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.1308 time to fit residues: 4.5191 Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8564 moved from start: 0.1932 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= 0.199 Angle : 0.462 8.099 5243 Z= 0.242 Chirality : 0.039 0.130 638 Planarity : 0.002 0.018 687 Dihedral : 3.667 17.719 552 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 12.87 % Favored : 86.14 % 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: 2.67 (0.37), residues: 522 helix: 2.83 (0.29), residues: 300 sheet: 1.06 (0.60), residues: 74 loop : -0.12 (0.48), 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 195 TYR 0.008 0.001 TYR B 506 ARG 0.001 0.000 ARG B 421 *********************** 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 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.484 Fit side-chains REVERT: B 193 MET cc_start: 0.8766 (ttm) cc_final: 0.8462 (ttm) REVERT: B 307 MET cc_start: 0.8459 (mpp) cc_final: 0.8070 (mpp) outliers start: 4 outliers final: 4 residues processed: 23 average time/residue: 0.1171 time to fit residues: 4.1386 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 89 THR 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: 2.9990 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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: 0.8554 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 : 0.003 0.024 3883 Z= 0.169 Angle : 0.449 8.924 5243 Z= 0.234 Chirality : 0.039 0.127 638 Planarity : 0.002 0.016 687 Dihedral : 3.621 17.641 552 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.49 % Allowed : 12.87 % Favored : 85.64 % 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: 2.72 (0.37), residues: 522 helix: 2.86 (0.29), residues: 300 sheet: 1.10 (0.60), residues: 74 loop : -0.08 (0.48), residues: 148 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 0.001 0.000 ARG B 421 *********************** 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 fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.374 Fit side-chains REVERT: B 193 MET cc_start: 0.8753 (ttm) cc_final: 0.8474 (ttm) REVERT: B 307 MET cc_start: 0.8458 (mpp) cc_final: 0.8089 (mpp) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.1250 time to fit residues: 5.2593 Evaluate side-chains 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET 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 24 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- 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: 0.8586 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3883 Z= 0.294 Angle : 0.512 9.616 5243 Z= 0.265 Chirality : 0.040 0.135 638 Planarity : 0.002 0.026 687 Dihedral : 3.713 17.357 552 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.73 % Allowed : 12.87 % Favored : 85.40 % 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: 2.62 (0.36), residues: 522 helix: 2.78 (0.29), residues: 300 sheet: 1.03 (0.60), residues: 74 loop : -0.13 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.010 0.002 PHE B 8 TYR 0.010 0.001 TYR B 506 ARG 0.003 0.000 ARG B 452 *********************** 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 fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.478 Fit side-chains REVERT: B 193 MET cc_start: 0.8797 (ttm) cc_final: 0.8486 (ttm) REVERT: B 307 MET cc_start: 0.8451 (mpp) cc_final: 0.8058 (mpp) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.1108 time to fit residues: 4.4515 Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- 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: 0.8543 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3883 Z= 0.123 Angle : 0.448 8.705 5243 Z= 0.235 Chirality : 0.039 0.127 638 Planarity : 0.002 0.017 687 Dihedral : 3.618 17.955 552 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.99 % Allowed : 13.37 % Favored : 85.64 % 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: 2.63 (0.36), residues: 522 helix: 2.79 (0.29), residues: 299 sheet: 1.10 (0.60), residues: 74 loop : -0.11 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 8 TYR 0.007 0.001 TYR B 199 ARG 0.003 0.000 ARG B 18 *********************** 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 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.475 Fit side-chains REVERT: B 16 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8854 (mtm) REVERT: B 193 MET cc_start: 0.8717 (ttm) cc_final: 0.8470 (ttm) REVERT: B 307 MET cc_start: 0.8422 (mpp) cc_final: 0.8061 (mpp) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1138 time to fit residues: 4.1969 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET 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=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: 10.0000 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- 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: 0.8564 moved from start: 0.2099 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= 0.189 Angle : 0.442 5.854 5243 Z= 0.233 Chirality : 0.039 0.128 638 Planarity : 0.002 0.019 687 Dihedral : 3.606 17.546 552 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.24 % Allowed : 12.62 % Favored : 86.14 % 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: 2.68 (0.36), residues: 522 helix: 2.80 (0.29), residues: 300 sheet: 1.15 (0.60), residues: 74 loop : -0.08 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.009 0.001 PHE B 8 TYR 0.009 0.001 TYR B 506 ARG 0.001 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 fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.481 Fit side-chains REVERT: B 193 MET cc_start: 0.8748 (ttm) cc_final: 0.8476 (ttm) REVERT: B 307 MET cc_start: 0.8431 (mpp) cc_final: 0.8068 (mpp) outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.1133 time to fit residues: 4.1849 Evaluate side-chains 23 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.061924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.048466 restraints weight = 12878.839| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.44 r_work: 0.2758 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3883 Z= 0.231 Angle : 0.490 10.797 5243 Z= 0.252 Chirality : 0.039 0.131 638 Planarity : 0.002 0.020 687 Dihedral : 3.692 17.680 552 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.99 % Allowed : 12.87 % Favored : 86.14 % 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: 2.64 (0.36), residues: 522 helix: 2.79 (0.29), residues: 300 sheet: 1.08 (0.61), residues: 74 loop : -0.11 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.009 0.001 PHE B 8 TYR 0.008 0.001 TYR B 506 ARG 0.002 0.000 ARG B 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1006.45 seconds wall clock time: 19 minutes 5.43 seconds (1145.43 seconds total)