Starting phenix.real_space_refine on Sun Mar 10 17:31:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/03_2024/8sc6_40339_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/03_2024/8sc6_40339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/03_2024/8sc6_40339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/03_2024/8sc6_40339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/03_2024/8sc6_40339_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/03_2024/8sc6_40339_updated.pdb" } resolution = 3.13 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= 0.034 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 31 5.16 5 C 2293 2.51 5 N 565 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3461 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.29, per 1000 atoms: 0.66 Number of scatterers: 3479 At special positions: 0 Unit cell: (90.72, 84, 68.04, 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 31 16.00 O 590 8.00 N 565 7.00 C 2293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 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: 1.44 Conformation dependent library (CDL) restraints added in 739.0 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 1 sheets defined 73.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 removed outlier: 4.213A pdb=" N ILE A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 42 removed outlier: 5.489A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 40 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.520A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS A 154 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.820A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 removed outlier: 3.738A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 257 removed outlier: 3.612A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 277 Proline residue: A 271 - end of helix removed outlier: 3.515A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.504A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 371 Processing helix chain 'A' and resid 375 through 397 removed outlier: 3.508A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.974A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 removed outlier: 3.738A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 490 removed outlier: 3.567A pdb=" N ARG A 462 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN A 463 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 464 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 480 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.584A pdb=" N VAL A 484 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 485 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 488 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.019A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 50 214 hydrogen bonds defined for protein. 516 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: 0.81 Time building geometry restraints manager: 1.56 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: 1071 1.34 - 1.46: 838 1.46 - 1.58: 1616 1.58 - 1.69: 1 1.69 - 1.81: 46 Bond restraints: 3572 Sorted by residual: bond pdb=" CA LEU A 427 " pdb=" C LEU A 427 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.14e-02 7.69e+03 5.00e-01 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.84e-01 bond pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 1.520 1.529 -0.008 1.23e-02 6.61e+03 4.75e-01 bond pdb=" C ALA A 257 " pdb=" N LEU A 258 " ideal model delta sigma weight residual 1.327 1.336 -0.009 1.32e-02 5.74e+03 4.45e-01 bond pdb=" C VAL A 461 " pdb=" O VAL A 461 " ideal model delta sigma weight residual 1.226 1.240 -0.013 2.04e-02 2.40e+03 4.30e-01 ... (remaining 3567 not shown) Histogram of bond angle deviations from ideal: 91.52 - 100.01: 1 100.01 - 108.49: 162 108.49 - 116.98: 2236 116.98 - 125.47: 2396 125.47 - 133.95: 75 Bond angle restraints: 4870 Sorted by residual: angle pdb=" C GLU A 386 " pdb=" N ILE A 387 " pdb=" CA ILE A 387 " ideal model delta sigma weight residual 120.33 122.81 -2.48 8.00e-01 1.56e+00 9.59e+00 angle pdb=" C TYR A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta sigma weight residual 122.46 117.60 4.86 1.80e+00 3.09e-01 7.30e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 119.23 -4.83 2.30e+00 1.89e-01 4.40e+00 angle pdb=" N THR A 480 " pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 112.75 115.58 -2.83 1.36e+00 5.41e-01 4.34e+00 angle pdb=" C VAL A 461 " pdb=" CA VAL A 461 " pdb=" CB VAL A 461 " ideal model delta sigma weight residual 112.36 109.75 2.61 1.37e+00 5.33e-01 3.62e+00 ... (remaining 4865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.01: 1882 11.01 - 22.02: 141 22.02 - 33.03: 34 33.03 - 44.04: 9 44.04 - 55.05: 1 Dihedral angle restraints: 2067 sinusoidal: 788 harmonic: 1279 Sorted by residual: dihedral pdb=" N PHE A 273 " pdb=" CA PHE A 273 " pdb=" CB PHE A 273 " pdb=" CG PHE A 273 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " pdb=" CG LEU A 150 " ideal model delta sinusoidal sigma weight residual -60.00 -102.93 42.93 3 1.50e+01 4.44e-03 7.71e+00 dihedral pdb=" N MET A 239 " pdb=" CA MET A 239 " pdb=" CB MET A 239 " pdb=" CG MET A 239 " ideal model delta sinusoidal sigma weight residual -180.00 -141.24 -38.76 3 1.50e+01 4.44e-03 6.84e+00 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 313 0.022 - 0.043: 148 0.043 - 0.065: 63 0.065 - 0.087: 18 0.087 - 0.109: 20 Chirality restraints: 562 Sorted by residual: chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA LEU A 270 " pdb=" N LEU A 270 " pdb=" C LEU A 270 " pdb=" CB LEU A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.88e-01 chirality pdb=" CA PRO A 53 " pdb=" N PRO A 53 " pdb=" C PRO A 53 " pdb=" CB PRO A 53 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 559 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO A 271 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 75 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 65 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 66 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.016 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 873 2.80 - 3.32: 3442 3.32 - 3.85: 5517 3.85 - 4.37: 6305 4.37 - 4.90: 11189 Nonbonded interactions: 27326 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.273 2.440 nonbonded pdb=" OE1 GLU A 137 " pdb=" NE1 TRP A 261 " model vdw 2.340 2.520 nonbonded pdb=" NZ LYS A 214 " pdb=" OD1 ASP A 474 " model vdw 2.351 2.520 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.353 2.440 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.363 2.440 ... (remaining 27321 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: 0.750 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: 3.680 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.240 Find NCS groups from input model: 0.090 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 0.023 3572 Z= 0.165 Angle : 0.502 5.291 4870 Z= 0.288 Chirality : 0.035 0.109 562 Planarity : 0.004 0.031 601 Dihedral : 8.707 55.052 1240 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.81 % Allowed : 2.96 % Favored : 96.23 % 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: 2.80 (0.41), residues: 443 helix: 2.09 (0.31), residues: 302 sheet: None (None), residues: 0 loop : 1.57 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 244 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.363 Fit side-chains REVERT: A 273 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: A 351 MET cc_start: 0.8709 (mtt) cc_final: 0.8385 (mtp) REVERT: A 357 ASP cc_start: 0.7980 (m-30) cc_final: 0.7731 (m-30) outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.1772 time to fit residues: 14.3804 Evaluate side-chains 41 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 115 HIS A 447 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3572 Z= 0.199 Angle : 0.485 6.702 4870 Z= 0.252 Chirality : 0.037 0.130 562 Planarity : 0.005 0.034 601 Dihedral : 4.700 53.649 487 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 9.97 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.42), residues: 443 helix: 2.02 (0.31), residues: 304 sheet: None (None), residues: 0 loop : 1.30 (0.58), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.009 0.001 TYR A 240 ARG 0.008 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.426 Fit side-chains REVERT: A 273 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: A 351 MET cc_start: 0.8712 (mtt) cc_final: 0.8494 (mtm) REVERT: A 357 ASP cc_start: 0.8015 (m-30) cc_final: 0.7777 (m-30) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.1421 time to fit residues: 8.9930 Evaluate side-chains 45 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 33 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.130 Angle : 0.423 5.181 4870 Z= 0.219 Chirality : 0.035 0.121 562 Planarity : 0.004 0.030 601 Dihedral : 4.544 54.304 487 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.89 % Allowed : 10.24 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.41), residues: 443 helix: 1.95 (0.31), residues: 305 sheet: None (None), residues: 0 loop : 1.10 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.008 0.001 TYR A 168 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.583 Fit side-chains REVERT: A 27 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7245 (tt) REVERT: A 273 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7642 (m-80) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.1277 time to fit residues: 7.5753 Evaluate side-chains 45 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.0030 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3572 Z= 0.178 Angle : 0.442 5.284 4870 Z= 0.228 Chirality : 0.036 0.119 562 Planarity : 0.004 0.029 601 Dihedral : 4.598 55.834 487 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.43 % Allowed : 10.24 % Favored : 87.33 % 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: 2.38 (0.41), residues: 443 helix: 1.82 (0.31), residues: 312 sheet: None (None), residues: 0 loop : 1.20 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.008 0.001 TYR A 168 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.373 Fit side-chains REVERT: A 273 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7622 (m-80) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.1435 time to fit residues: 8.9172 Evaluate side-chains 50 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3572 Z= 0.154 Angle : 0.432 5.346 4870 Z= 0.222 Chirality : 0.035 0.117 562 Planarity : 0.004 0.028 601 Dihedral : 4.560 56.808 487 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.96 % Allowed : 10.51 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.42), residues: 443 helix: 1.88 (0.31), residues: 312 sheet: None (None), residues: 0 loop : 1.18 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 244 TYR 0.008 0.001 TYR A 352 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.326 Fit side-chains REVERT: A 273 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7522 (m-80) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.1347 time to fit residues: 8.5336 Evaluate side-chains 50 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3572 Z= 0.162 Angle : 0.440 5.298 4870 Z= 0.225 Chirality : 0.035 0.116 562 Planarity : 0.004 0.028 601 Dihedral : 4.576 58.156 487 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.70 % Allowed : 11.05 % Favored : 86.25 % 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: 2.38 (0.42), residues: 443 helix: 1.87 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.07 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.007 0.001 TYR A 352 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.331 Fit side-chains REVERT: A 273 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7550 (m-80) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.1334 time to fit residues: 8.0441 Evaluate side-chains 48 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 8 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.135 Angle : 0.419 5.252 4870 Z= 0.215 Chirality : 0.035 0.115 562 Planarity : 0.004 0.027 601 Dihedral : 4.521 58.312 487 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.23 % Allowed : 10.78 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.42), residues: 443 helix: 1.95 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.14 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 244 TYR 0.007 0.001 TYR A 352 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.411 Fit side-chains REVERT: A 273 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7503 (m-80) outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 0.1603 time to fit residues: 10.8613 Evaluate side-chains 50 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3572 Z= 0.173 Angle : 0.447 5.655 4870 Z= 0.227 Chirality : 0.036 0.115 562 Planarity : 0.004 0.028 601 Dihedral : 4.599 59.651 487 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.96 % Allowed : 10.78 % Favored : 86.25 % 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: 2.37 (0.42), residues: 443 helix: 1.87 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.05 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.008 0.001 PHE A 244 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.732 Fit side-chains REVERT: A 273 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: A 492 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7834 (tp-100) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.2204 time to fit residues: 14.7471 Evaluate side-chains 51 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.0060 chunk 41 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.002 0.019 3572 Z= 0.113 Angle : 0.416 5.259 4870 Z= 0.212 Chirality : 0.034 0.114 562 Planarity : 0.004 0.027 601 Dihedral : 4.513 59.201 487 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.16 % Allowed : 12.67 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.42), residues: 443 helix: 1.98 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.14 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.008 0.001 PHE A 244 TYR 0.006 0.001 TYR A 352 ARG 0.001 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.385 Fit side-chains REVERT: A 273 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: A 395 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7405 (mm) REVERT: A 492 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7815 (tp-100) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1291 time to fit residues: 7.8774 Evaluate side-chains 47 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 9 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3572 Z= 0.154 Angle : 0.435 5.334 4870 Z= 0.222 Chirality : 0.035 0.114 562 Planarity : 0.004 0.027 601 Dihedral : 4.557 59.534 487 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.89 % Allowed : 13.21 % Favored : 84.91 % 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: 2.44 (0.42), residues: 443 helix: 1.93 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.09 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 244 TYR 0.007 0.001 TYR A 352 ARG 0.001 0.000 ARG A 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.325 Fit side-chains REVERT: A 273 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: A 492 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7863 (tp-100) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.1168 time to fit residues: 6.8286 Evaluate side-chains 46 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.0070 overall best weight: 0.2426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.196628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139335 restraints weight = 3534.073| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.10 r_work: 0.3228 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3572 Z= 0.109 Angle : 0.405 5.207 4870 Z= 0.206 Chirality : 0.034 0.114 562 Planarity : 0.004 0.027 601 Dihedral : 4.484 59.947 487 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.62 % Allowed : 13.75 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.42), residues: 443 helix: 1.99 (0.31), residues: 311 sheet: None (None), residues: 0 loop : 1.16 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.009 0.001 PHE A 244 TYR 0.006 0.001 TYR A 168 ARG 0.000 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.49 seconds wall clock time: 23 minutes 28.92 seconds (1408.92 seconds total)