Starting phenix.real_space_refine on Thu Nov 14 01:38:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jdv_61399/11_2024/9jdv_61399_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jdv_61399/11_2024/9jdv_61399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jdv_61399/11_2024/9jdv_61399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jdv_61399/11_2024/9jdv_61399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jdv_61399/11_2024/9jdv_61399_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jdv_61399/11_2024/9jdv_61399_trim.cif" } resolution = 3.32 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= 0.003 sd= 0.060 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 28 5.16 5 C 2164 2.51 5 N 558 2.21 5 O 561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3298 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 26, 'TRANS': 408} Chain breaks: 4 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.85, per 1000 atoms: 0.86 Number of scatterers: 3311 At special positions: 0 Unit cell: (94.17, 51.1, 66.43, 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 28 16.00 O 561 8.00 N 558 7.00 C 2164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 380.3 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 82.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 4.267A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.069A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 191 Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.801A pdb=" N ALA A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 273 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.858A pdb=" N ARG A 342 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.601A pdb=" N LEU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix removed outlier: 4.255A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 removed outlier: 3.515A pdb=" N THR A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 4.070A pdb=" N SER A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 465 No H-bonds generated for 'chain 'A' and resid 464 through 465' Processing helix chain 'A' and resid 467 through 467 No H-bonds generated for 'chain 'A' and resid 467 through 467' Processing helix chain 'A' and resid 468 through 487 Proline residue: A 484 - end of helix removed outlier: 3.548A pdb=" N ARG A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.573A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 Proline residue: A 505 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.723A pdb=" N ARG A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 684 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: 0.93 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 499 1.30 - 1.43: 900 1.43 - 1.55: 1954 1.55 - 1.68: 0 1.68 - 1.81: 44 Bond restraints: 3397 Sorted by residual: bond pdb=" CA SER A 242 " pdb=" C SER A 242 " ideal model delta sigma weight residual 1.523 1.438 0.086 1.34e-02 5.57e+03 4.08e+01 bond pdb=" C4 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.352 1.465 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" N PHE A 241 " pdb=" CA PHE A 241 " ideal model delta sigma weight residual 1.457 1.387 0.070 1.29e-02 6.01e+03 2.97e+01 bond pdb=" C4 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.352 1.456 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.376 1.478 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 3392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 4555 2.10 - 4.20: 55 4.20 - 6.30: 20 6.30 - 8.40: 6 8.40 - 10.50: 2 Bond angle restraints: 4638 Sorted by residual: angle pdb=" N ARG A 477 " pdb=" CA ARG A 477 " pdb=" C ARG A 477 " ideal model delta sigma weight residual 111.14 104.52 6.62 1.08e+00 8.57e-01 3.76e+01 angle pdb=" C ALA A 476 " pdb=" N ARG A 477 " pdb=" CA ARG A 477 " ideal model delta sigma weight residual 120.44 115.34 5.10 1.36e+00 5.41e-01 1.41e+01 angle pdb=" N PHE A 241 " pdb=" CA PHE A 241 " pdb=" C PHE A 241 " ideal model delta sigma weight residual 110.80 103.28 7.52 2.13e+00 2.20e-01 1.25e+01 angle pdb=" C2 URC A 601 " pdb=" N1 URC A 601 " pdb=" C6 URC A 601 " ideal model delta sigma weight residual 129.31 118.81 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C SER A 266 " pdb=" N VAL A 267 " pdb=" CA VAL A 267 " ideal model delta sigma weight residual 120.24 122.31 -2.07 6.30e-01 2.52e+00 1.08e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1775 17.81 - 35.63: 156 35.63 - 53.44: 32 53.44 - 71.25: 5 71.25 - 89.07: 3 Dihedral angle restraints: 1971 sinusoidal: 735 harmonic: 1236 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -140.99 54.99 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 127.97 -34.97 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" C SER A 242 " pdb=" N SER A 242 " pdb=" CA SER A 242 " pdb=" CB SER A 242 " ideal model delta harmonic sigma weight residual -122.60 -114.32 -8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 1968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 347 0.027 - 0.054: 129 0.054 - 0.081: 43 0.081 - 0.108: 23 0.108 - 0.135: 2 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA VAL A 426 " pdb=" N VAL A 426 " pdb=" C VAL A 426 " pdb=" CB VAL A 426 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" C PRO A 268 " pdb=" CB PRO A 268 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 541 not shown) Planarity restraints: 572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 239 " 0.027 2.00e-02 2.50e+03 5.59e-02 3.13e+01 pdb=" C LEU A 239 " -0.097 2.00e-02 2.50e+03 pdb=" O LEU A 239 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY A 240 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 241 " -0.005 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE A 241 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 241 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 241 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 241 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 241 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 241 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 268 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.016 5.00e-02 4.00e+02 ... (remaining 569 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 77 2.70 - 3.25: 3402 3.25 - 3.80: 5480 3.80 - 4.35: 6879 4.35 - 4.90: 11201 Nonbonded interactions: 27039 Sorted by model distance: nonbonded pdb=" O GLY A 240 " pdb=" C PHE A 241 " model vdw 2.150 3.270 nonbonded pdb=" CE2 PHE A 241 " pdb=" O13 URC A 601 " model vdw 2.168 2.672 nonbonded pdb=" O PHE A 241 " pdb=" C SER A 242 " model vdw 2.240 3.270 nonbonded pdb=" O SER A 242 " pdb=" N HIS A 245 " model vdw 2.262 3.120 nonbonded pdb=" O GLY A 240 " pdb=" N PHE A 243 " model vdw 2.272 3.120 ... (remaining 27034 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 0.006 0.113 3397 Z= 0.409 Angle : 0.706 10.503 4638 Z= 0.385 Chirality : 0.035 0.135 544 Planarity : 0.004 0.056 572 Dihedral : 13.991 89.067 1167 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.03 % Allowed : 9.28 % Favored : 88.70 % 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: -0.41 (0.40), residues: 425 helix: 0.02 (0.29), residues: 289 sheet: -2.23 (1.36), residues: 10 loop : -0.44 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 30 HIS 0.001 0.000 HIS A 428 PHE 0.023 0.001 PHE A 241 TYR 0.003 0.001 TYR A 152 ARG 0.001 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.367 Fit side-chains REVERT: A 29 MET cc_start: 0.7581 (ttp) cc_final: 0.7280 (ttp) REVERT: A 96 TRP cc_start: 0.4546 (m100) cc_final: 0.4252 (m-10) REVERT: A 343 MET cc_start: 0.2977 (tpt) cc_final: 0.1234 (tpp) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.1534 time to fit residues: 19.6960 Evaluate side-chains 74 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 424 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 39 ASN A 382 GLN A 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3397 Z= 0.292 Angle : 0.695 7.486 4638 Z= 0.334 Chirality : 0.045 0.146 544 Planarity : 0.005 0.027 572 Dihedral : 5.434 55.606 464 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.64 % Allowed : 19.71 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.43), residues: 425 helix: 0.94 (0.31), residues: 297 sheet: -1.89 (1.53), residues: 10 loop : 0.63 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.007 0.001 HIS A 47 PHE 0.022 0.003 PHE A 40 TYR 0.022 0.002 TYR A 122 ARG 0.004 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4815 (m100) cc_final: 0.4290 (m-10) REVERT: A 181 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7116 (tt) REVERT: A 234 MET cc_start: 0.7478 (tpp) cc_final: 0.7248 (tpp) REVERT: A 343 MET cc_start: 0.3050 (tpt) cc_final: 0.1385 (tpp) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.1004 time to fit residues: 11.7422 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 38 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3397 Z= 0.172 Angle : 0.610 7.660 4638 Z= 0.288 Chirality : 0.040 0.120 544 Planarity : 0.004 0.031 572 Dihedral : 5.267 54.020 463 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 23.77 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.43), residues: 425 helix: 1.48 (0.31), residues: 296 sheet: -2.20 (1.65), residues: 10 loop : 1.09 (0.67), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 495 HIS 0.002 0.001 HIS A 47 PHE 0.019 0.002 PHE A 358 TYR 0.007 0.001 TYR A 122 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4724 (m100) cc_final: 0.4218 (m-10) REVERT: A 181 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6996 (tt) REVERT: A 343 MET cc_start: 0.2911 (tpt) cc_final: 0.1253 (tpp) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.1016 time to fit residues: 10.6612 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3397 Z= 0.225 Angle : 0.628 7.084 4638 Z= 0.302 Chirality : 0.041 0.129 544 Planarity : 0.004 0.036 572 Dihedral : 4.879 41.812 463 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.35 % Allowed : 24.06 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.43), residues: 425 helix: 1.54 (0.31), residues: 296 sheet: -2.23 (1.75), residues: 10 loop : 1.08 (0.67), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 50 HIS 0.004 0.001 HIS A 47 PHE 0.016 0.002 PHE A 358 TYR 0.015 0.002 TYR A 122 ARG 0.004 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ILE cc_start: 0.4322 (OUTLIER) cc_final: 0.3716 (tt) REVERT: A 96 TRP cc_start: 0.4677 (m100) cc_final: 0.4110 (m-10) REVERT: A 181 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7073 (tt) REVERT: A 215 MET cc_start: 0.7559 (tpp) cc_final: 0.7310 (tpp) REVERT: A 343 MET cc_start: 0.2976 (tpt) cc_final: 0.1359 (tpp) REVERT: A 421 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7694 (mp) outliers start: 15 outliers final: 9 residues processed: 78 average time/residue: 0.1044 time to fit residues: 10.7857 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3397 Z= 0.215 Angle : 0.609 8.151 4638 Z= 0.295 Chirality : 0.041 0.121 544 Planarity : 0.004 0.030 572 Dihedral : 4.738 48.859 462 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.93 % Allowed : 24.93 % Favored : 70.14 % 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: 2.02 (0.44), residues: 425 helix: 1.64 (0.31), residues: 296 sheet: -2.28 (1.78), residues: 10 loop : 1.19 (0.69), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 50 HIS 0.003 0.001 HIS A 492 PHE 0.016 0.002 PHE A 241 TYR 0.014 0.002 TYR A 152 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7809 (ttm) cc_final: 0.7583 (ttp) REVERT: A 96 TRP cc_start: 0.4732 (m100) cc_final: 0.4118 (m-10) REVERT: A 181 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7002 (tt) REVERT: A 215 MET cc_start: 0.7670 (tpp) cc_final: 0.7406 (tpp) REVERT: A 343 MET cc_start: 0.2847 (tpt) cc_final: 0.1188 (tpp) REVERT: A 372 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7863 (tp-100) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.1007 time to fit residues: 10.8853 Evaluate side-chains 75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3397 Z= 0.165 Angle : 0.585 8.016 4638 Z= 0.282 Chirality : 0.040 0.118 544 Planarity : 0.004 0.032 572 Dihedral : 4.654 50.346 462 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.35 % Allowed : 27.25 % Favored : 68.41 % 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: 2.06 (0.44), residues: 425 helix: 1.72 (0.31), residues: 295 sheet: -2.31 (1.83), residues: 10 loop : 1.04 (0.68), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 50 HIS 0.002 0.001 HIS A 86 PHE 0.012 0.001 PHE A 241 TYR 0.012 0.001 TYR A 152 ARG 0.001 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7766 (ttm) cc_final: 0.7530 (ttp) REVERT: A 96 TRP cc_start: 0.4723 (m100) cc_final: 0.4100 (m-10) REVERT: A 181 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6978 (tt) REVERT: A 215 MET cc_start: 0.7734 (tpp) cc_final: 0.7451 (tpp) REVERT: A 343 MET cc_start: 0.2804 (tpt) cc_final: 0.1155 (tpp) REVERT: A 372 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7830 (tp-100) outliers start: 15 outliers final: 7 residues processed: 82 average time/residue: 0.1040 time to fit residues: 11.5125 Evaluate side-chains 73 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3397 Z= 0.178 Angle : 0.588 7.322 4638 Z= 0.287 Chirality : 0.040 0.127 544 Planarity : 0.004 0.032 572 Dihedral : 4.465 51.438 461 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.06 % Allowed : 28.12 % Favored : 67.83 % 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: 2.12 (0.44), residues: 425 helix: 1.72 (0.31), residues: 296 sheet: -2.32 (1.79), residues: 10 loop : 1.20 (0.70), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 50 HIS 0.002 0.001 HIS A 86 PHE 0.016 0.002 PHE A 360 TYR 0.011 0.001 TYR A 152 ARG 0.001 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.4703 (m100) cc_final: 0.4065 (m-10) REVERT: A 181 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6936 (tt) REVERT: A 215 MET cc_start: 0.7744 (tpp) cc_final: 0.7450 (tpp) REVERT: A 343 MET cc_start: 0.2873 (tpt) cc_final: 0.1239 (tpp) REVERT: A 352 ILE cc_start: 0.7963 (mm) cc_final: 0.7751 (mm) REVERT: A 372 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7829 (tp-100) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.1117 time to fit residues: 11.4397 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3397 Z= 0.211 Angle : 0.611 7.619 4638 Z= 0.298 Chirality : 0.041 0.115 544 Planarity : 0.004 0.034 572 Dihedral : 4.572 53.248 461 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.22 % Allowed : 27.25 % Favored : 67.54 % 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: 2.11 (0.44), residues: 425 helix: 1.72 (0.31), residues: 294 sheet: -2.17 (1.80), residues: 10 loop : 1.19 (0.68), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.002 0.001 HIS A 245 PHE 0.016 0.002 PHE A 241 TYR 0.012 0.001 TYR A 152 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7759 (ttm) cc_final: 0.7539 (ttp) REVERT: A 96 TRP cc_start: 0.4813 (m100) cc_final: 0.4116 (m-10) REVERT: A 181 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7019 (tt) REVERT: A 215 MET cc_start: 0.7808 (tpp) cc_final: 0.7505 (tpp) REVERT: A 343 MET cc_start: 0.2879 (tpt) cc_final: 0.1277 (tpp) REVERT: A 372 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7870 (tp-100) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.1111 time to fit residues: 12.0169 Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.6987 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3397 Z= 0.212 Angle : 0.640 6.376 4638 Z= 0.315 Chirality : 0.042 0.150 544 Planarity : 0.004 0.033 572 Dihedral : 4.638 54.600 461 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.35 % Allowed : 28.70 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.44), residues: 425 helix: 1.61 (0.31), residues: 294 sheet: -2.30 (1.79), residues: 10 loop : 1.20 (0.69), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 50 HIS 0.002 0.001 HIS A 86 PHE 0.015 0.002 PHE A 449 TYR 0.017 0.001 TYR A 152 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7748 (ttm) cc_final: 0.7524 (ttp) REVERT: A 96 TRP cc_start: 0.4738 (m100) cc_final: 0.4056 (m-10) REVERT: A 181 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7053 (tt) REVERT: A 215 MET cc_start: 0.7805 (tpp) cc_final: 0.7506 (tpp) REVERT: A 343 MET cc_start: 0.2812 (tpt) cc_final: 0.1232 (tpp) REVERT: A 372 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7878 (tp-100) outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.1130 time to fit residues: 11.6200 Evaluate side-chains 84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.6950 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3397 Z= 0.187 Angle : 0.647 7.362 4638 Z= 0.313 Chirality : 0.042 0.147 544 Planarity : 0.004 0.034 572 Dihedral : 4.609 56.656 461 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.06 % Allowed : 29.28 % Favored : 66.67 % 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: 2.01 (0.44), residues: 425 helix: 1.66 (0.31), residues: 294 sheet: -2.50 (1.82), residues: 10 loop : 1.14 (0.68), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 50 HIS 0.003 0.001 HIS A 86 PHE 0.016 0.002 PHE A 360 TYR 0.015 0.001 TYR A 152 ARG 0.001 0.000 ARG A 477 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.5174 (tpp) cc_final: 0.4806 (tpp) REVERT: A 29 MET cc_start: 0.7721 (ttm) cc_final: 0.7511 (ttp) REVERT: A 96 TRP cc_start: 0.4715 (m100) cc_final: 0.4129 (m-10) REVERT: A 181 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7005 (tt) REVERT: A 215 MET cc_start: 0.7788 (tpp) cc_final: 0.7498 (tpp) REVERT: A 343 MET cc_start: 0.2691 (tpt) cc_final: 0.1365 (tpp) REVERT: A 372 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7860 (tp-100) outliers start: 14 outliers final: 13 residues processed: 79 average time/residue: 0.1182 time to fit residues: 12.2034 Evaluate side-chains 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.218842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.184636 restraints weight = 4345.938| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 3.33 r_work: 0.4160 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3397 Z= 0.192 Angle : 0.629 6.659 4638 Z= 0.309 Chirality : 0.041 0.137 544 Planarity : 0.004 0.032 572 Dihedral : 4.608 56.887 461 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.35 % Allowed : 29.57 % Favored : 66.09 % 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: 2.00 (0.44), residues: 425 helix: 1.65 (0.31), residues: 294 sheet: -2.61 (1.83), residues: 10 loop : 1.14 (0.68), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 50 HIS 0.002 0.001 HIS A 86 PHE 0.014 0.002 PHE A 360 TYR 0.014 0.001 TYR A 152 ARG 0.001 0.000 ARG A 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1111.14 seconds wall clock time: 20 minutes 53.88 seconds (1253.88 seconds total)