Starting phenix.real_space_refine on Mon Sep 23 16:08:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j77_36030/09_2024/8j77_36030.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j77_36030/09_2024/8j77_36030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j77_36030/09_2024/8j77_36030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j77_36030/09_2024/8j77_36030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j77_36030/09_2024/8j77_36030.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j77_36030/09_2024/8j77_36030.cif" } resolution = 3.7 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= 0.157 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 19 5.16 5 C 2513 2.51 5 N 577 2.21 5 O 669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3778 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3732 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 470} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.73, per 1000 atoms: 0.99 Number of scatterers: 3778 At special positions: 0 Unit cell: (86.1, 69.7, 91.02, 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 19 16.00 O 669 8.00 N 577 7.00 C 2513 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 491.3 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 74.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 3 through 28 Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.775A pdb=" N TRP A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 85 through 103 removed outlier: 4.763A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 107 removed outlier: 3.514A pdb=" N ARG A 107 " --> pdb=" O LYS A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 107' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.538A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 158 removed outlier: 3.926A pdb=" N LEU A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.577A pdb=" N ALA A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.945A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.526A pdb=" N PHE A 258 " --> pdb=" O TRP A 254 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 298 removed outlier: 3.912A pdb=" N ALA A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.637A pdb=" N ILE A 291 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 367 removed outlier: 3.699A pdb=" N PHE A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 397 Processing helix chain 'A' and resid 402 through 417 removed outlier: 4.261A pdb=" N TRP A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.746A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.752A pdb=" N ASN A 474 " --> pdb=" O TYR A 466 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 566 1.29 - 1.42: 1080 1.42 - 1.55: 2197 1.55 - 1.68: 3 1.68 - 1.81: 34 Bond restraints: 3880 Sorted by residual: bond pdb=" C TRP A 62 " pdb=" O TRP A 62 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.16e-02 7.43e+03 4.63e+01 bond pdb=" CA TRP A 62 " pdb=" CB TRP A 62 " ideal model delta sigma weight residual 1.529 1.444 0.085 1.58e-02 4.01e+03 2.87e+01 bond pdb=" CA TRP A 62 " pdb=" C TRP A 62 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.26e-02 6.30e+03 2.02e+01 bond pdb=" N TRP A 62 " pdb=" CA TRP A 62 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" C THR A 61 " pdb=" N TRP A 62 " ideal model delta sigma weight residual 1.334 1.290 0.044 1.33e-02 5.65e+03 1.09e+01 ... (remaining 3875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 5240 4.16 - 8.32: 57 8.32 - 12.48: 3 12.48 - 16.64: 0 16.64 - 20.81: 2 Bond angle restraints: 5302 Sorted by residual: angle pdb=" N ALA A 222 " pdb=" CA ALA A 222 " pdb=" C ALA A 222 " ideal model delta sigma weight residual 110.91 131.72 -20.81 1.17e+00 7.31e-01 3.16e+02 angle pdb=" N GLY A 123 " pdb=" CA GLY A 123 " pdb=" C GLY A 123 " ideal model delta sigma weight residual 111.73 93.88 17.85 1.73e+00 3.34e-01 1.06e+02 angle pdb=" N SER A 367 " pdb=" CA SER A 367 " pdb=" C SER A 367 " ideal model delta sigma weight residual 110.97 118.10 -7.13 1.09e+00 8.42e-01 4.28e+01 angle pdb=" C ALA A 222 " pdb=" CA ALA A 222 " pdb=" CB ALA A 222 " ideal model delta sigma weight residual 112.27 100.85 11.42 1.75e+00 3.27e-01 4.26e+01 angle pdb=" CA THR A 61 " pdb=" C THR A 61 " pdb=" N TRP A 62 " ideal model delta sigma weight residual 117.30 123.91 -6.61 1.16e+00 7.43e-01 3.25e+01 ... (remaining 5297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 2086 21.80 - 43.59: 126 43.59 - 65.39: 10 65.39 - 87.19: 10 87.19 - 108.98: 4 Dihedral angle restraints: 2236 sinusoidal: 820 harmonic: 1416 Sorted by residual: dihedral pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA LYS A 428 " pdb=" C LYS A 428 " pdb=" N GLY A 429 " pdb=" CA GLY A 429 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA TYR A 364 " pdb=" C TYR A 364 " pdb=" N GLN A 365 " pdb=" CA GLN A 365 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 596 0.102 - 0.205: 25 0.205 - 0.307: 3 0.307 - 0.410: 0 0.410 - 0.512: 2 Chirality restraints: 626 Sorted by residual: chirality pdb=" CA ALA A 222 " pdb=" N ALA A 222 " pdb=" C ALA A 222 " pdb=" CB ALA A 222 " both_signs ideal model delta sigma weight residual False 2.48 1.97 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 623 not shown) Planarity restraints: 643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 221 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C HIS A 221 " -0.054 2.00e-02 2.50e+03 pdb=" O HIS A 221 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 222 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 377 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C ILE A 377 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE A 377 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 378 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 314 " 0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C GLU A 314 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 314 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 315 " 0.011 2.00e-02 2.50e+03 ... (remaining 640 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 92 2.70 - 3.25: 3949 3.25 - 3.80: 5988 3.80 - 4.35: 7159 4.35 - 4.90: 12071 Nonbonded interactions: 29259 Sorted by model distance: nonbonded pdb=" NH1 ARG A 369 " pdb=" O GLN A 370 " model vdw 2.149 3.120 nonbonded pdb=" OH TYR A 91 " pdb=" OG SER A 410 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP A 188 " pdb=" OE1 GLN A 191 " model vdw 2.244 3.040 nonbonded pdb=" O ALA A 343 " pdb=" OG SER A 346 " model vdw 2.269 3.040 nonbonded pdb=" NH1 ARG A 125 " pdb=" O LEU A 366 " model vdw 2.296 3.120 ... (remaining 29254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 0.085 3880 Z= 0.364 Angle : 1.029 20.805 5302 Z= 0.616 Chirality : 0.057 0.512 626 Planarity : 0.005 0.047 642 Dihedral : 15.385 108.985 1338 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % 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: -0.89 (0.39), residues: 487 helix: 0.90 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -3.56 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 62 HIS 0.006 0.002 HIS A 162 PHE 0.014 0.002 PHE A 14 TYR 0.019 0.002 TYR A 67 ARG 0.004 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.424 Fit side-chains REVERT: A 284 MET cc_start: 0.7773 (tpp) cc_final: 0.7381 (tpt) REVERT: A 403 TYR cc_start: 0.8519 (t80) cc_final: 0.8116 (t80) REVERT: A 484 MET cc_start: 0.8101 (tmm) cc_final: 0.7529 (ttt) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1566 time to fit residues: 13.0503 Evaluate side-chains 57 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3880 Z= 0.231 Angle : 0.736 9.413 5302 Z= 0.374 Chirality : 0.044 0.322 626 Planarity : 0.005 0.042 642 Dihedral : 9.260 65.473 592 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.21 % Favored : 91.58 % Rotamer: Outliers : 1.59 % Allowed : 9.28 % Favored : 89.12 % 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: -0.47 (0.40), residues: 487 helix: 1.34 (0.30), residues: 314 sheet: -1.71 (1.52), residues: 10 loop : -3.76 (0.43), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 254 HIS 0.007 0.002 HIS A 221 PHE 0.016 0.002 PHE A 244 TYR 0.019 0.002 TYR A 67 ARG 0.003 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.378 Fit side-chains REVERT: A 76 TYR cc_start: 0.8688 (t80) cc_final: 0.8324 (t80) REVERT: A 161 MET cc_start: 0.6635 (tmm) cc_final: 0.5767 (tpt) REVERT: A 242 ASP cc_start: 0.7897 (t70) cc_final: 0.7630 (t0) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.1437 time to fit residues: 10.9156 Evaluate side-chains 52 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 345 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3880 Z= 0.221 Angle : 0.697 9.473 5302 Z= 0.354 Chirality : 0.044 0.323 626 Planarity : 0.004 0.043 642 Dihedral : 7.357 56.921 592 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.39 % Allowed : 15.38 % Favored : 82.23 % 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: -0.20 (0.41), residues: 487 helix: 1.54 (0.30), residues: 314 sheet: -1.71 (1.55), residues: 10 loop : -3.60 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 406 HIS 0.003 0.001 HIS A 162 PHE 0.025 0.002 PHE A 386 TYR 0.014 0.001 TYR A 364 ARG 0.003 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.383 Fit side-chains REVERT: A 76 TYR cc_start: 0.8693 (t80) cc_final: 0.8437 (t80) REVERT: A 106 MET cc_start: 0.8314 (tpt) cc_final: 0.8000 (tpt) REVERT: A 161 MET cc_start: 0.6629 (tmm) cc_final: 0.5833 (tpt) REVERT: A 242 ASP cc_start: 0.7857 (t70) cc_final: 0.7657 (t0) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.1518 time to fit residues: 12.4041 Evaluate side-chains 56 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3880 Z= 0.202 Angle : 0.676 9.547 5302 Z= 0.342 Chirality : 0.042 0.323 626 Planarity : 0.004 0.041 642 Dihedral : 6.996 58.867 592 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.92 % Allowed : 17.77 % Favored : 79.31 % 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: -0.07 (0.41), residues: 487 helix: 1.64 (0.30), residues: 313 sheet: -1.64 (1.60), residues: 10 loop : -3.53 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 406 HIS 0.003 0.001 HIS A 162 PHE 0.020 0.001 PHE A 386 TYR 0.011 0.001 TYR A 111 ARG 0.005 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.379 Fit side-chains REVERT: A 76 TYR cc_start: 0.8672 (t80) cc_final: 0.8465 (t80) REVERT: A 106 MET cc_start: 0.8205 (tpt) cc_final: 0.7969 (tpt) REVERT: A 161 MET cc_start: 0.6553 (tmm) cc_final: 0.6113 (tpp) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.1317 time to fit residues: 9.5828 Evaluate side-chains 57 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3880 Z= 0.208 Angle : 0.672 9.545 5302 Z= 0.338 Chirality : 0.042 0.322 626 Planarity : 0.004 0.040 642 Dihedral : 6.831 57.899 592 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.98 % Allowed : 18.30 % Favored : 77.72 % 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: -0.01 (0.41), residues: 487 helix: 1.68 (0.30), residues: 313 sheet: -1.54 (1.65), residues: 10 loop : -3.49 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 27 HIS 0.003 0.001 HIS A 162 PHE 0.018 0.001 PHE A 386 TYR 0.018 0.001 TYR A 111 ARG 0.005 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.342 Fit side-chains REVERT: A 76 TYR cc_start: 0.8665 (t80) cc_final: 0.8448 (t80) REVERT: A 161 MET cc_start: 0.6485 (tmm) cc_final: 0.5765 (tpt) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.1253 time to fit residues: 9.7699 Evaluate side-chains 54 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.0050 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3880 Z= 0.179 Angle : 0.651 9.549 5302 Z= 0.330 Chirality : 0.041 0.316 626 Planarity : 0.004 0.038 642 Dihedral : 6.613 55.964 592 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.98 % Allowed : 18.30 % Favored : 77.72 % 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: 0.11 (0.41), residues: 487 helix: 1.73 (0.30), residues: 315 sheet: -1.41 (1.69), residues: 10 loop : -3.43 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 27 HIS 0.003 0.001 HIS A 162 PHE 0.017 0.001 PHE A 386 TYR 0.015 0.001 TYR A 111 ARG 0.003 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 0.388 Fit side-chains REVERT: A 62 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7059 (m-90) REVERT: A 161 MET cc_start: 0.6465 (tmm) cc_final: 0.5998 (tpp) REVERT: A 207 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.5991 (pt) outliers start: 15 outliers final: 9 residues processed: 56 average time/residue: 0.1258 time to fit residues: 9.4254 Evaluate side-chains 54 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3880 Z= 0.162 Angle : 0.630 9.559 5302 Z= 0.317 Chirality : 0.041 0.314 626 Planarity : 0.004 0.036 642 Dihedral : 6.423 56.212 592 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.86 % Allowed : 21.49 % Favored : 76.66 % 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: 0.30 (0.41), residues: 487 helix: 1.97 (0.30), residues: 310 sheet: -1.40 (1.72), residues: 10 loop : -3.38 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 PHE 0.014 0.001 PHE A 386 TYR 0.015 0.001 TYR A 111 ARG 0.004 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.379 Fit side-chains REVERT: A 62 TRP cc_start: 0.8119 (OUTLIER) cc_final: 0.7186 (m-90) REVERT: A 161 MET cc_start: 0.6428 (tmm) cc_final: 0.6014 (tpt) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.1348 time to fit residues: 9.2144 Evaluate side-chains 50 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 411 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3880 Z= 0.198 Angle : 0.645 9.547 5302 Z= 0.323 Chirality : 0.041 0.324 626 Planarity : 0.004 0.036 642 Dihedral : 6.381 56.020 592 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.18 % Allowed : 20.16 % Favored : 76.66 % 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: 0.27 (0.41), residues: 487 helix: 1.96 (0.30), residues: 310 sheet: -1.53 (1.71), residues: 10 loop : -3.42 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 PHE 0.014 0.001 PHE A 386 TYR 0.013 0.001 TYR A 111 ARG 0.004 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.393 Fit side-chains REVERT: A 62 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.7258 (m-90) REVERT: A 161 MET cc_start: 0.6454 (tmm) cc_final: 0.6008 (tpt) REVERT: A 207 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5797 (pt) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.1461 time to fit residues: 9.6876 Evaluate side-chains 48 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 411 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3880 Z= 0.169 Angle : 0.635 9.533 5302 Z= 0.317 Chirality : 0.041 0.316 626 Planarity : 0.004 0.035 642 Dihedral : 6.316 56.198 592 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.45 % Allowed : 19.89 % Favored : 76.66 % 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: 0.40 (0.41), residues: 487 helix: 2.07 (0.30), residues: 310 sheet: -1.40 (1.74), residues: 10 loop : -3.40 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 PHE 0.012 0.001 PHE A 334 TYR 0.012 0.001 TYR A 111 ARG 0.003 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8125 (OUTLIER) cc_final: 0.7382 (t-100) REVERT: A 161 MET cc_start: 0.6443 (tmm) cc_final: 0.5587 (tpt) REVERT: A 207 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5632 (pt) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.1136 time to fit residues: 8.1034 Evaluate side-chains 51 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3880 Z= 0.168 Angle : 0.631 9.529 5302 Z= 0.314 Chirality : 0.041 0.319 626 Planarity : 0.004 0.035 642 Dihedral : 6.170 56.344 592 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.65 % Allowed : 20.69 % Favored : 76.66 % 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: 0.50 (0.42), residues: 487 helix: 2.16 (0.30), residues: 310 sheet: -1.39 (1.81), residues: 10 loop : -3.38 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 PHE 0.013 0.001 PHE A 244 TYR 0.013 0.001 TYR A 111 ARG 0.003 0.000 ARG A 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.6394 (tmm) cc_final: 0.5477 (tpt) REVERT: A 207 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5412 (pt) REVERT: A 242 ASP cc_start: 0.7803 (t70) cc_final: 0.7594 (t0) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.1251 time to fit residues: 8.7407 Evaluate side-chains 53 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 44 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.183821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.165083 restraints weight = 4411.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.167674 restraints weight = 2987.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.169189 restraints weight = 2267.173| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3880 Z= 0.150 Angle : 0.615 9.545 5302 Z= 0.305 Chirality : 0.040 0.304 626 Planarity : 0.004 0.035 642 Dihedral : 5.674 56.873 590 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.39 % Allowed : 20.69 % Favored : 76.92 % 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: 0.61 (0.42), residues: 487 helix: 2.26 (0.30), residues: 310 sheet: -1.52 (1.81), residues: 10 loop : -3.34 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 406 HIS 0.002 0.001 HIS A 162 PHE 0.011 0.001 PHE A 244 TYR 0.011 0.001 TYR A 111 ARG 0.003 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1122.18 seconds wall clock time: 20 minutes 35.29 seconds (1235.29 seconds total)