Starting phenix.real_space_refine on Fri Aug 2 17:07:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/08_2024/8qvw_18674.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/08_2024/8qvw_18674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/08_2024/8qvw_18674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/08_2024/8qvw_18674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/08_2024/8qvw_18674.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qvw_18674/08_2024/8qvw_18674.cif" } resolution = 3.0 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= 0.002 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 18 5.16 5 C 2484 2.51 5 N 680 2.21 5 O 736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3918 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 451 Classifications: {'peptide': 56} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 47} Chain: "B" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3467 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 2 Time building chain proxies: 2.65, per 1000 atoms: 0.68 Number of scatterers: 3918 At special positions: 0 Unit cell: (115.14, 72.96, 70.68, 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 18 16.00 O 736 8.00 N 680 7.00 C 2484 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: 1.43 Conformation dependent library (CDL) restraints added in 650.0 milliseconds 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 956 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.678A pdb=" N LEU A 595 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.936A pdb=" N LEU A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 27 through 41 Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 60 through 76 removed outlier: 5.121A pdb=" N LYS B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 76 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.779A pdb=" N LYS B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 143 through 162 Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 192 through 211 removed outlier: 3.513A pdb=" N MET B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 197 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.587A pdb=" N ILE B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 256 removed outlier: 3.557A pdb=" N LYS B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 278 through 290 removed outlier: 3.607A pdb=" N LYS B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 320 through 333 removed outlier: 3.599A pdb=" N GLN B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.756A pdb=" N GLU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 removed outlier: 3.889A pdb=" N ILE B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.619A pdb=" N GLU B 419 " --> pdb=" O MET B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 443 through 460 271 hydrogen bonds defined for protein. 792 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: 0.99 Time building geometry restraints manager: 1.59 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: 1306 1.34 - 1.46: 560 1.46 - 1.58: 2093 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3983 Sorted by residual: bond pdb=" CB PHE A 561 " pdb=" CG PHE A 561 " ideal model delta sigma weight residual 1.502 1.531 -0.029 2.30e-02 1.89e+03 1.58e+00 bond pdb=" CB ASN B 318 " pdb=" CG ASN B 318 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.56e+00 bond pdb=" CA ASN B 318 " pdb=" CB ASN B 318 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.14e+00 bond pdb=" CB GLU B 427 " pdb=" CG GLU B 427 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CA GLU B 427 " pdb=" CB GLU B 427 " ideal model delta sigma weight residual 1.528 1.544 -0.015 1.59e-02 3.96e+03 9.26e-01 ... (remaining 3978 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.79: 70 105.79 - 112.84: 2178 112.84 - 119.89: 1351 119.89 - 126.94: 1746 126.94 - 133.99: 38 Bond angle restraints: 5383 Sorted by residual: angle pdb=" C ALA B 76 " pdb=" CA ALA B 76 " pdb=" CB ALA B 76 " ideal model delta sigma weight residual 115.79 109.95 5.84 1.19e+00 7.06e-01 2.41e+01 angle pdb=" CA GLU B 427 " pdb=" CB GLU B 427 " pdb=" CG GLU B 427 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" C LEU A 563 " pdb=" N ASP A 564 " pdb=" CA ASP A 564 " ideal model delta sigma weight residual 121.80 129.42 -7.62 2.44e+00 1.68e-01 9.76e+00 angle pdb=" CA LEU B 402 " pdb=" CB LEU B 402 " pdb=" CG LEU B 402 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.50e+00 angle pdb=" N GLN B 353 " pdb=" CA GLN B 353 " pdb=" C GLN B 353 " ideal model delta sigma weight residual 109.71 106.19 3.52 1.41e+00 5.03e-01 6.24e+00 ... (remaining 5378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 2081 17.63 - 35.26: 288 35.26 - 52.89: 74 52.89 - 70.51: 15 70.51 - 88.14: 9 Dihedral angle restraints: 2467 sinusoidal: 1008 harmonic: 1459 Sorted by residual: dihedral pdb=" CA ASN B 388 " pdb=" CB ASN B 388 " pdb=" CG ASN B 388 " pdb=" OD1 ASN B 388 " ideal model delta sinusoidal sigma weight residual -90.00 -164.64 74.64 2 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA LYS B 383 " pdb=" C LYS B 383 " pdb=" N ILE B 384 " pdb=" CA ILE B 384 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLU B 351 " pdb=" C GLU B 351 " pdb=" N LYS B 352 " pdb=" CA LYS B 352 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 2464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 445 0.039 - 0.078: 142 0.078 - 0.116: 30 0.116 - 0.155: 2 0.155 - 0.194: 1 Chirality restraints: 620 Sorted by residual: chirality pdb=" CG LEU B 402 " pdb=" CB LEU B 402 " pdb=" CD1 LEU B 402 " pdb=" CD2 LEU B 402 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA ASN B 318 " pdb=" N ASN B 318 " pdb=" C ASN B 318 " pdb=" CB ASN B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ASP A 564 " pdb=" N ASP A 564 " pdb=" C ASP A 564 " pdb=" CB ASP A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 617 not shown) Planarity restraints: 694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 561 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C PHE A 561 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE A 561 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS A 562 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 598 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.09e+00 pdb=" C VAL A 598 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL A 598 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A 599 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 21 " 0.010 2.00e-02 2.50e+03 8.27e-03 1.37e+00 pdb=" CG TYR B 21 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 21 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 21 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 21 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 21 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 21 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 21 " 0.000 2.00e-02 2.50e+03 ... (remaining 691 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 97 2.70 - 3.25: 4250 3.25 - 3.80: 6680 3.80 - 4.35: 8170 4.35 - 4.90: 13230 Nonbonded interactions: 32427 Sorted by model distance: nonbonded pdb=" O PRO B 406 " pdb=" OG SER B 410 " model vdw 2.155 3.040 nonbonded pdb=" N GLU B 146 " pdb=" OE1 GLU B 146 " model vdw 2.247 3.120 nonbonded pdb=" O ASN B 278 " pdb=" OG SER B 282 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP B 141 " pdb=" NH1 ARG B 147 " model vdw 2.286 3.120 nonbonded pdb=" O LEU B 313 " pdb=" OG1 THR B 317 " model vdw 2.299 3.040 ... (remaining 32422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.250 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.003 0.036 3983 Z= 0.179 Angle : 0.601 8.925 5383 Z= 0.318 Chirality : 0.038 0.194 620 Planarity : 0.003 0.027 694 Dihedral : 18.024 88.143 1511 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.23 % Allowed : 25.12 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.40), residues: 484 helix: 1.20 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.20 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.011 0.001 PHE A 561 TYR 0.020 0.001 TYR B 21 ARG 0.006 0.001 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 TYR cc_start: 0.6012 (t80) cc_final: 0.4898 (t80) REVERT: B 408 MET cc_start: 0.7442 (ttt) cc_final: 0.7130 (ttt) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.9194 time to fit residues: 62.3758 Evaluate side-chains 59 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN B 92 ASN B 274 ASN B 278 ASN B 302 GLN B 304 GLN B 309 ASN B 322 GLN B 333 GLN B 347 GLN B 353 GLN B 439 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3983 Z= 0.186 Angle : 0.568 7.435 5383 Z= 0.294 Chirality : 0.039 0.135 620 Planarity : 0.003 0.028 694 Dihedral : 3.995 16.525 520 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.76 % Allowed : 25.35 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.39), residues: 484 helix: 1.36 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.01 (0.66), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.002 0.001 HIS B 439 PHE 0.011 0.001 PHE B 429 TYR 0.016 0.001 TYR B 132 ARG 0.003 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 GLN cc_start: 0.7766 (pt0) cc_final: 0.7545 (pt0) REVERT: B 137 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6827 (ttp-170) REVERT: B 366 ASP cc_start: 0.7766 (m-30) cc_final: 0.7561 (m-30) REVERT: B 408 MET cc_start: 0.7373 (ttt) cc_final: 0.7022 (ttt) REVERT: B 427 GLU cc_start: 0.8422 (pp20) cc_final: 0.7999 (pp20) outliers start: 12 outliers final: 3 residues processed: 71 average time/residue: 1.0401 time to fit residues: 76.7412 Evaluate side-chains 60 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3983 Z= 0.196 Angle : 0.570 8.065 5383 Z= 0.292 Chirality : 0.039 0.141 620 Planarity : 0.003 0.022 694 Dihedral : 3.936 15.777 520 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.15 % Allowed : 25.35 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.39), residues: 484 helix: 1.35 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.08 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.012 0.001 PHE B 429 TYR 0.007 0.001 TYR B 86 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 TYR cc_start: 0.5162 (t80) cc_final: 0.4504 (t80) REVERT: B 23 GLN cc_start: 0.7870 (pt0) cc_final: 0.7592 (pt0) REVERT: B 29 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7326 (mtm180) REVERT: B 132 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 366 ASP cc_start: 0.7790 (m-30) cc_final: 0.7552 (m-30) REVERT: B 408 MET cc_start: 0.7317 (ttt) cc_final: 0.6985 (ttt) REVERT: B 427 GLU cc_start: 0.8341 (pp20) cc_final: 0.8069 (pp20) outliers start: 18 outliers final: 4 residues processed: 71 average time/residue: 0.9055 time to fit residues: 67.2371 Evaluate side-chains 61 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 132 TYR Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 354 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3983 Z= 0.203 Angle : 0.568 7.542 5383 Z= 0.289 Chirality : 0.039 0.140 620 Planarity : 0.003 0.024 694 Dihedral : 3.914 15.195 520 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.69 % Allowed : 25.81 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.39), residues: 484 helix: 1.23 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.00 (0.66), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.014 0.001 PHE B 429 TYR 0.008 0.001 TYR B 86 ARG 0.003 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 LEU cc_start: 0.6863 (mt) cc_final: 0.6488 (mt) REVERT: B 23 GLN cc_start: 0.7891 (pt0) cc_final: 0.7617 (pt0) REVERT: B 178 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8231 (tt) REVERT: B 208 ARG cc_start: 0.8166 (mmp80) cc_final: 0.7873 (mpp-170) REVERT: B 366 ASP cc_start: 0.7798 (m-30) cc_final: 0.7529 (m-30) REVERT: B 408 MET cc_start: 0.7391 (ttt) cc_final: 0.7028 (ttt) REVERT: B 427 GLU cc_start: 0.8446 (pp20) cc_final: 0.7953 (pp20) outliers start: 16 outliers final: 5 residues processed: 74 average time/residue: 0.9841 time to fit residues: 75.9868 Evaluate side-chains 64 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 354 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3983 Z= 0.209 Angle : 0.596 8.191 5383 Z= 0.302 Chirality : 0.040 0.151 620 Planarity : 0.003 0.038 694 Dihedral : 3.957 14.978 520 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.76 % Allowed : 27.42 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.38), residues: 484 helix: 1.15 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.03 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE B 429 TYR 0.013 0.001 TYR B 21 ARG 0.007 0.001 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 LEU cc_start: 0.6823 (mt) cc_final: 0.6225 (mp) REVERT: B 178 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 208 ARG cc_start: 0.8154 (mmp80) cc_final: 0.7848 (mpp-170) REVERT: B 366 ASP cc_start: 0.7830 (m-30) cc_final: 0.7555 (m-30) REVERT: B 382 LEU cc_start: 0.8235 (mm) cc_final: 0.7940 (mm) REVERT: B 408 MET cc_start: 0.7320 (ttt) cc_final: 0.6969 (ttt) REVERT: B 427 GLU cc_start: 0.8430 (pp20) cc_final: 0.8218 (pp20) outliers start: 12 outliers final: 6 residues processed: 66 average time/residue: 0.9641 time to fit residues: 66.3454 Evaluate side-chains 60 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7548 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3983 Z= 0.208 Angle : 0.599 9.119 5383 Z= 0.300 Chirality : 0.040 0.171 620 Planarity : 0.003 0.036 694 Dihedral : 3.939 14.889 520 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.23 % Allowed : 27.19 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.39), residues: 484 helix: 1.13 (0.26), residues: 379 sheet: None (None), residues: 0 loop : 0.06 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE B 429 TYR 0.010 0.001 TYR B 86 ARG 0.009 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8277 (mmtt) REVERT: A 607 LEU cc_start: 0.6728 (mt) cc_final: 0.6140 (mp) REVERT: B 178 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8244 (tt) REVERT: B 208 ARG cc_start: 0.8142 (mmp80) cc_final: 0.7831 (mpp-170) REVERT: B 366 ASP cc_start: 0.7793 (m-30) cc_final: 0.7552 (m-30) REVERT: B 382 LEU cc_start: 0.8218 (mm) cc_final: 0.7924 (mm) REVERT: B 408 MET cc_start: 0.7310 (ttt) cc_final: 0.6903 (ttt) outliers start: 14 outliers final: 7 residues processed: 68 average time/residue: 0.9362 time to fit residues: 66.7408 Evaluate side-chains 62 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN B 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3983 Z= 0.178 Angle : 0.600 9.943 5383 Z= 0.301 Chirality : 0.039 0.169 620 Planarity : 0.003 0.031 694 Dihedral : 3.899 15.091 520 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.23 % Allowed : 28.11 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.39), residues: 484 helix: 1.16 (0.26), residues: 381 sheet: None (None), residues: 0 loop : 0.06 (0.68), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.015 0.001 PHE B 429 TYR 0.008 0.001 TYR B 86 ARG 0.008 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 595 LEU cc_start: 0.8716 (tp) cc_final: 0.8480 (tp) REVERT: A 607 LEU cc_start: 0.6647 (mt) cc_final: 0.6115 (mp) REVERT: B 178 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8226 (tt) REVERT: B 208 ARG cc_start: 0.8125 (mmp80) cc_final: 0.7841 (mpp-170) REVERT: B 366 ASP cc_start: 0.7793 (m-30) cc_final: 0.7559 (m-30) REVERT: B 408 MET cc_start: 0.7298 (ttt) cc_final: 0.6874 (ttt) REVERT: B 415 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7943 (ttm) outliers start: 14 outliers final: 9 residues processed: 67 average time/residue: 0.8192 time to fit residues: 57.6153 Evaluate side-chains 63 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3983 Z= 0.185 Angle : 0.599 9.894 5383 Z= 0.304 Chirality : 0.039 0.173 620 Planarity : 0.003 0.030 694 Dihedral : 3.864 14.185 520 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.23 % Allowed : 28.57 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.39), residues: 484 helix: 1.18 (0.26), residues: 383 sheet: None (None), residues: 0 loop : 0.14 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.012 0.001 PHE B 429 TYR 0.009 0.001 TYR B 21 ARG 0.007 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 595 LEU cc_start: 0.8742 (tp) cc_final: 0.8501 (tp) REVERT: A 607 LEU cc_start: 0.6706 (mt) cc_final: 0.6176 (mp) REVERT: B 35 ASN cc_start: 0.8020 (p0) cc_final: 0.7784 (p0) REVERT: B 178 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8228 (tt) REVERT: B 366 ASP cc_start: 0.7788 (m-30) cc_final: 0.7551 (m-30) REVERT: B 408 MET cc_start: 0.7306 (ttt) cc_final: 0.6883 (ttt) REVERT: B 415 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7943 (ttm) outliers start: 14 outliers final: 7 residues processed: 68 average time/residue: 0.8387 time to fit residues: 59.8643 Evaluate side-chains 68 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7541 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3983 Z= 0.209 Angle : 0.650 11.254 5383 Z= 0.326 Chirality : 0.039 0.137 620 Planarity : 0.003 0.037 694 Dihedral : 3.923 16.065 520 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.46 % Allowed : 28.11 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.39), residues: 484 helix: 1.12 (0.26), residues: 381 sheet: None (None), residues: 0 loop : 0.20 (0.69), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.002 0.001 HIS B 404 PHE 0.012 0.001 PHE B 429 TYR 0.009 0.001 TYR B 132 ARG 0.007 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 LEU cc_start: 0.6814 (mt) cc_final: 0.6246 (mp) REVERT: B 178 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8250 (tt) REVERT: B 366 ASP cc_start: 0.7882 (m-30) cc_final: 0.7640 (m-30) REVERT: B 382 LEU cc_start: 0.8221 (mm) cc_final: 0.7916 (mm) REVERT: B 408 MET cc_start: 0.7408 (ttt) cc_final: 0.7005 (ttt) REVERT: B 415 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7944 (ttm) outliers start: 15 outliers final: 9 residues processed: 66 average time/residue: 0.8630 time to fit residues: 59.8154 Evaluate side-chains 66 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.0060 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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: 0.7522 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3983 Z= 0.196 Angle : 0.699 11.575 5383 Z= 0.342 Chirality : 0.040 0.153 620 Planarity : 0.003 0.028 694 Dihedral : 3.947 17.393 520 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.00 % Allowed : 29.03 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.39), residues: 484 helix: 1.12 (0.26), residues: 384 sheet: None (None), residues: 0 loop : 0.19 (0.71), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.012 0.001 PHE B 429 TYR 0.009 0.001 TYR B 86 ARG 0.006 0.001 ARG B 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 595 LEU cc_start: 0.8688 (tp) cc_final: 0.8440 (tp) REVERT: A 607 LEU cc_start: 0.6796 (mt) cc_final: 0.6582 (mp) REVERT: B 19 ASN cc_start: 0.8160 (t0) cc_final: 0.7641 (p0) REVERT: B 178 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8220 (tt) REVERT: B 366 ASP cc_start: 0.7851 (m-30) cc_final: 0.7614 (m-30) REVERT: B 408 MET cc_start: 0.7300 (ttt) cc_final: 0.6910 (ttt) REVERT: B 415 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7938 (ttm) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.7967 time to fit residues: 53.7231 Evaluate side-chains 64 residues out of total 434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.146837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118256 restraints weight = 7343.653| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.67 r_work: 0.3562 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3983 Z= 0.232 Angle : 0.701 11.645 5383 Z= 0.345 Chirality : 0.041 0.137 620 Planarity : 0.003 0.023 694 Dihedral : 3.995 17.618 520 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.69 % Allowed : 29.26 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.39), residues: 484 helix: 1.07 (0.26), residues: 382 sheet: None (None), residues: 0 loop : 0.20 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.003 0.001 HIS B 404 PHE 0.010 0.001 PHE B 429 TYR 0.010 0.001 TYR B 86 ARG 0.006 0.001 ARG B 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.09 seconds wall clock time: 29 minutes 53.25 seconds (1793.25 seconds total)