Starting phenix.real_space_refine on Fri Apr 5 14:09:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/04_2024/8ju0_36658_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/04_2024/8ju0_36658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/04_2024/8ju0_36658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/04_2024/8ju0_36658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/04_2024/8ju0_36658_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/04_2024/8ju0_36658_updated.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.171 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 2117 2.51 5 N 519 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 123": "OD1" <-> "OD2" Residue "A ASP 144": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3199 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3170 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SNL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.67 Number of scatterers: 3199 At special positions: 0 Unit cell: (58.455, 90.93, 68.1975, 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 532 8.00 N 519 7.00 C 2117 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: 1.38 Conformation dependent library (CDL) restraints added in 624.9 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 1 sheets defined 74.9% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 24 through 36 Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.639A pdb=" N LEU A 42 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 66 through 72 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 105 through 109 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 195 removed outlier: 4.539A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 154 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 162 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP A 171 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ARG A 175 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS A 176 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU A 177 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS A 178 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 188 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 226 removed outlier: 3.942A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 257 Processing helix chain 'A' and resid 261 through 274 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 341 through 371 Processing helix chain 'A' and resid 375 through 399 Proline residue: A 388 - end of helix removed outlier: 4.174A pdb=" N PHE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.674A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 455 removed outlier: 3.623A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 490 Proline residue: A 481 - end of helix removed outlier: 4.396A pdb=" N ARG A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.030A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 4.626A 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 50 212 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 478 1.31 - 1.43: 893 1.43 - 1.56: 1865 1.56 - 1.69: 2 1.69 - 1.81: 45 Bond restraints: 3283 Sorted by residual: bond pdb=" C15 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.332 1.545 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C22 SNL A 601 " pdb=" S61 SNL A 601 " ideal model delta sigma weight residual 1.829 1.651 0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" C16 SNL A 601 " pdb=" S61 SNL A 601 " ideal model delta sigma weight residual 1.767 1.677 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.443 1.518 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C18 SNL A 601 " pdb=" C19 SNL A 601 " ideal model delta sigma weight residual 1.463 1.537 -0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 3278 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.70: 59 103.70 - 111.34: 1468 111.34 - 118.97: 1159 118.97 - 126.61: 1742 126.61 - 134.24: 66 Bond angle restraints: 4494 Sorted by residual: angle pdb=" C13 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" C5 SNL A 601 " ideal model delta sigma weight residual 116.85 134.24 -17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C8 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 111.01 96.07 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C16 SNL A 601 " pdb=" S61 SNL A 601 " pdb=" C22 SNL A 601 " ideal model delta sigma weight residual 101.80 115.41 -13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C1 SNL A 601 " pdb=" C2 SNL A 601 " pdb=" C24 SNL A 601 " ideal model delta sigma weight residual 108.42 117.77 -9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" C5 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 111.22 102.15 9.07 3.00e+00 1.11e-01 9.15e+00 ... (remaining 4489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 1722 14.26 - 28.52: 156 28.52 - 42.77: 52 42.77 - 57.03: 15 57.03 - 71.29: 5 Dihedral angle restraints: 1950 sinusoidal: 721 harmonic: 1229 Sorted by residual: dihedral pdb=" SG CYS A 50 " pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" CA CYS A 121 " ideal model delta sinusoidal sigma weight residual 79.00 9.30 69.70 1 2.00e+01 2.50e-03 1.57e+01 dihedral pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " ideal model delta sinusoidal sigma weight residual -73.00 -11.22 -61.78 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CA ASN A 453 " pdb=" CB ASN A 453 " pdb=" CG ASN A 453 " pdb=" OD1 ASN A 453 " ideal model delta sinusoidal sigma weight residual 120.00 -172.00 -68.00 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 531 0.181 - 0.362: 3 0.362 - 0.542: 0 0.542 - 0.723: 1 0.723 - 0.904: 1 Chirality restraints: 536 Sorted by residual: chirality pdb=" C9 SNL A 601 " pdb=" C13 SNL A 601 " pdb=" C5 SNL A 601 " pdb=" C8 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.67 -1.77 -0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C2 SNL A 601 " pdb=" C1 SNL A 601 " pdb=" C20 SNL A 601 " pdb=" C24 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.82 -2.20 -0.62 2.00e-01 2.50e+01 9.56e+00 chirality pdb=" C6 SNL A 601 " pdb=" C23 SNL A 601 " pdb=" C5 SNL A 601 " pdb=" C7 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.43 -2.71 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 533 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 340 " -0.032 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO A 341 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO A 271 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 158 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C GLY A 158 " -0.027 2.00e-02 2.50e+03 pdb=" O GLY A 158 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 159 " 0.009 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 493 2.76 - 3.29: 3248 3.29 - 3.83: 5532 3.83 - 4.36: 6221 4.36 - 4.90: 10890 Nonbonded interactions: 26384 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.221 2.440 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.240 2.440 nonbonded pdb=" O HIS A 367 " pdb=" OG1 THR A 371 " model vdw 2.246 2.440 nonbonded pdb=" O MET A 368 " pdb=" OG SER A 372 " model vdw 2.374 2.440 nonbonded pdb=" O ASN A 71 " pdb=" NH2 ARG A 113 " model vdw 2.375 2.520 ... (remaining 26379 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: 0.330 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: 1.850 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.280 Find NCS groups from input model: 0.090 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:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 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 0.213 3283 Z= 0.475 Angle : 0.811 17.392 4494 Z= 0.350 Chirality : 0.063 0.904 536 Planarity : 0.004 0.050 551 Dihedral : 13.409 71.290 1153 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.42), residues: 425 helix: 1.50 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.12 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.016 0.001 TYR A 240 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.317 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.6345 time to fit residues: 29.0020 Evaluate side-chains 33 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3283 Z= 0.224 Angle : 0.532 5.584 4494 Z= 0.269 Chirality : 0.037 0.119 536 Planarity : 0.005 0.048 551 Dihedral : 5.400 29.770 529 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 9.62 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.42), residues: 425 helix: 1.46 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -0.03 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE A 44 TYR 0.015 0.001 TYR A 240 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.344 Fit side-chains REVERT: A 144 ASP cc_start: 0.7767 (m-30) cc_final: 0.7375 (m-30) REVERT: A 193 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7249 (tpp) REVERT: A 447 GLN cc_start: 0.7462 (mm110) cc_final: 0.7185 (mm110) outliers start: 7 outliers final: 3 residues processed: 39 average time/residue: 0.7305 time to fit residues: 30.1913 Evaluate side-chains 38 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3283 Z= 0.213 Angle : 0.518 6.158 4494 Z= 0.258 Chirality : 0.037 0.119 536 Planarity : 0.005 0.046 551 Dihedral : 4.888 28.219 529 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.56 % Allowed : 11.86 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.42), residues: 425 helix: 1.43 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.07 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 44 TYR 0.013 0.001 TYR A 240 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.336 Fit side-chains REVERT: A 144 ASP cc_start: 0.7822 (m-30) cc_final: 0.7446 (m-30) REVERT: A 447 GLN cc_start: 0.7461 (mm110) cc_final: 0.7221 (mm110) REVERT: A 448 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8283 (mpp) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 0.7376 time to fit residues: 30.3638 Evaluate side-chains 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3283 Z= 0.225 Angle : 0.523 6.239 4494 Z= 0.261 Chirality : 0.037 0.116 536 Planarity : 0.005 0.044 551 Dihedral : 4.747 27.450 529 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.24 % Allowed : 13.46 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.42), residues: 425 helix: 1.35 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.07 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.012 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.345 Fit side-chains REVERT: A 144 ASP cc_start: 0.7859 (m-30) cc_final: 0.7493 (m-30) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.6977 time to fit residues: 28.7704 Evaluate side-chains 37 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3283 Z= 0.160 Angle : 0.489 6.061 4494 Z= 0.244 Chirality : 0.036 0.117 536 Planarity : 0.004 0.043 551 Dihedral : 4.504 27.709 529 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 13.14 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.42), residues: 425 helix: 1.47 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -0.03 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.338 Fit side-chains REVERT: A 144 ASP cc_start: 0.7840 (m-30) cc_final: 0.7470 (m-30) REVERT: A 435 MET cc_start: 0.7494 (tpp) cc_final: 0.7243 (tpp) REVERT: A 447 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7340 (mm110) REVERT: A 448 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8101 (mpp) outliers start: 8 outliers final: 4 residues processed: 40 average time/residue: 0.7320 time to fit residues: 30.8977 Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3283 Z= 0.194 Angle : 0.509 6.398 4494 Z= 0.251 Chirality : 0.036 0.117 536 Planarity : 0.004 0.042 551 Dihedral : 4.480 28.817 529 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.88 % Allowed : 13.78 % Favored : 83.33 % 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: 1.56 (0.42), residues: 425 helix: 1.46 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.02 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.348 Fit side-chains REVERT: A 144 ASP cc_start: 0.7850 (m-30) cc_final: 0.7473 (m-30) REVERT: A 435 MET cc_start: 0.7652 (tpp) cc_final: 0.7387 (tpp) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 0.7230 time to fit residues: 30.5348 Evaluate side-chains 39 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3283 Z= 0.204 Angle : 0.524 6.650 4494 Z= 0.257 Chirality : 0.037 0.123 536 Planarity : 0.004 0.042 551 Dihedral : 4.541 27.953 529 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.24 % Allowed : 15.06 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.42), residues: 425 helix: 1.44 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.02 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 354 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.343 Fit side-chains REVERT: A 144 ASP cc_start: 0.7846 (m-30) cc_final: 0.7478 (m-30) REVERT: A 435 MET cc_start: 0.7660 (tpp) cc_final: 0.7394 (tpp) REVERT: A 447 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7401 (mm110) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.6946 time to fit residues: 29.3360 Evaluate side-chains 42 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 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 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3283 Z= 0.212 Angle : 0.539 7.013 4494 Z= 0.265 Chirality : 0.037 0.131 536 Planarity : 0.004 0.041 551 Dihedral : 4.496 27.416 529 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.53 % Allowed : 14.10 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.42), residues: 425 helix: 1.44 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.09 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 354 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.352 Fit side-chains REVERT: A 144 ASP cc_start: 0.7886 (m-30) cc_final: 0.7532 (m-30) REVERT: A 435 MET cc_start: 0.7662 (tpp) cc_final: 0.7390 (tpp) outliers start: 11 outliers final: 6 residues processed: 38 average time/residue: 0.6855 time to fit residues: 27.5373 Evaluate side-chains 38 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3283 Z= 0.247 Angle : 0.566 7.170 4494 Z= 0.276 Chirality : 0.038 0.130 536 Planarity : 0.004 0.041 551 Dihedral : 4.624 25.117 529 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.42), residues: 425 helix: 1.38 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -0.10 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 354 HIS 0.003 0.001 HIS A 49 PHE 0.012 0.001 PHE A 44 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.315 Fit side-chains REVERT: A 144 ASP cc_start: 0.7903 (m-30) cc_final: 0.7546 (m-30) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.6589 time to fit residues: 27.9352 Evaluate side-chains 38 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.0010 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3283 Z= 0.186 Angle : 0.544 7.013 4494 Z= 0.268 Chirality : 0.037 0.138 536 Planarity : 0.004 0.041 551 Dihedral : 4.463 24.626 529 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.56 % Allowed : 16.03 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.42), residues: 425 helix: 1.51 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -0.27 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.001 0.000 ARG A 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.333 Fit side-chains REVERT: A 144 ASP cc_start: 0.7875 (m-30) cc_final: 0.7503 (m-30) REVERT: A 420 MET cc_start: 0.8154 (mtp) cc_final: 0.7462 (mtt) REVERT: A 435 MET cc_start: 0.7647 (tpp) cc_final: 0.7392 (tpp) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.7205 time to fit residues: 28.1430 Evaluate side-chains 39 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.161094 restraints weight = 2996.907| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.65 r_work: 0.3553 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3283 Z= 0.203 Angle : 0.558 7.518 4494 Z= 0.272 Chirality : 0.037 0.135 536 Planarity : 0.004 0.041 551 Dihedral : 4.445 24.599 529 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 16.35 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.42), residues: 425 helix: 1.49 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -0.26 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 354 HIS 0.003 0.001 HIS A 49 PHE 0.011 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.001 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1323.09 seconds wall clock time: 24 minutes 37.07 seconds (1477.07 seconds total)