Starting phenix.real_space_refine on Thu Jul 18 19:07:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/07_2024/8ju0_36658.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/07_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_36658/07_2024/8ju0_36658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/07_2024/8ju0_36658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/07_2024/8ju0_36658.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ju0_36658/07_2024/8ju0_36658.cif" } 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-5388/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: 2.64, per 1000 atoms: 0.83 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: 1.74 Conformation dependent library (CDL) restraints added in 577.1 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... Secondary structure from input PDB file: 21 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 23 through 37 removed outlier: 3.573A pdb=" N LEU A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.683A pdb=" N SER A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 194 removed outlier: 4.073A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ARG A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N LYS A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 227 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 258 Processing helix chain 'A' and resid 260 through 275 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.835A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 400 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 402 through 423 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 428 through 456 removed outlier: 3.623A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 488 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) Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' 235 hydrogen bonds defined for protein. 699 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: 0.89 Time building geometry restraints manager: 1.45 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: 489 2.76 - 3.29: 3209 3.29 - 3.83: 5529 3.83 - 4.36: 6174 4.36 - 4.90: 10891 Nonbonded interactions: 26292 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 26287 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: 0.340 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- 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= 0.459 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 : 0.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.5842 time to fit residues: 26.6775 Evaluate side-chains 33 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7020 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3283 Z= 0.260 Angle : 0.556 5.468 4494 Z= 0.280 Chirality : 0.038 0.121 536 Planarity : 0.004 0.048 551 Dihedral : 5.235 26.018 529 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.24 % Allowed : 10.58 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.42), residues: 425 helix: 1.71 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.06 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 354 HIS 0.003 0.001 HIS A 260 PHE 0.011 0.001 PHE A 44 TYR 0.016 0.001 TYR A 240 ARG 0.004 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 42 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.252 Fit side-chains REVERT: A 447 GLN cc_start: 0.7486 (mm110) cc_final: 0.7186 (mm110) REVERT: A 448 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8262 (mpp) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.6459 time to fit residues: 25.9413 Evaluate side-chains 37 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1110 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= 0.214 Angle : 0.517 5.785 4494 Z= 0.261 Chirality : 0.037 0.121 536 Planarity : 0.004 0.046 551 Dihedral : 4.963 28.391 529 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.92 % Allowed : 12.18 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.43), residues: 425 helix: 1.87 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.08 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.335 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.7016 time to fit residues: 28.1773 Evaluate side-chains 37 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3283 Z= 0.276 Angle : 0.546 5.480 4494 Z= 0.275 Chirality : 0.038 0.125 536 Planarity : 0.004 0.044 551 Dihedral : 4.788 24.397 529 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.88 % Allowed : 15.06 % 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: 1.92 (0.42), residues: 425 helix: 1.77 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.06 (0.64), residues: 112 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 0.011 0.001 PHE A 44 TYR 0.011 0.001 TYR A 240 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 44 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.336 Fit side-chains REVERT: A 447 GLN cc_start: 0.7533 (mm110) cc_final: 0.7315 (mm110) REVERT: A 448 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8229 (mpp) outliers start: 9 outliers final: 7 residues processed: 41 average time/residue: 0.7001 time to fit residues: 30.3904 Evaluate side-chains 42 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 400 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 0.0060 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3283 Z= 0.170 Angle : 0.493 5.991 4494 Z= 0.249 Chirality : 0.036 0.119 536 Planarity : 0.004 0.043 551 Dihedral : 4.455 26.045 529 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 16.35 % 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: 2.13 (0.43), residues: 425 helix: 1.97 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.17 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 44 TYR 0.011 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 43 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.332 Fit side-chains REVERT: A 144 ASP cc_start: 0.7824 (m-30) cc_final: 0.7461 (m-30) REVERT: A 435 MET cc_start: 0.7519 (tpp) cc_final: 0.7280 (tpp) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.6815 time to fit residues: 28.8318 Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 472 LEU 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: 0.0070 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1364 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= 0.195 Angle : 0.509 6.333 4494 Z= 0.255 Chirality : 0.037 0.120 536 Planarity : 0.004 0.042 551 Dihedral : 4.395 26.918 529 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.43), residues: 425 helix: 2.00 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.12 (0.64), 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 0.009 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 42 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.328 Fit side-chains REVERT: A 435 MET cc_start: 0.7505 (tpp) cc_final: 0.7228 (tpp) REVERT: A 448 MET cc_start: 0.8339 (mpp) cc_final: 0.8065 (mpp) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.7410 time to fit residues: 29.6550 Evaluate side-chains 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.0010 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1429 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= 0.196 Angle : 0.505 6.755 4494 Z= 0.253 Chirality : 0.037 0.117 536 Planarity : 0.004 0.042 551 Dihedral : 4.366 27.088 529 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.88 % Allowed : 16.99 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.43), residues: 425 helix: 2.04 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.11 (0.64), 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 0.011 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 44 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.337 Fit side-chains REVERT: A 420 MET cc_start: 0.8237 (mtp) cc_final: 0.7580 (mtt) REVERT: A 435 MET cc_start: 0.7613 (tpp) cc_final: 0.7343 (tpp) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.6588 time to fit residues: 28.5953 Evaluate side-chains 39 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7025 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3283 Z= 0.236 Angle : 0.532 6.912 4494 Z= 0.264 Chirality : 0.038 0.120 536 Planarity : 0.004 0.041 551 Dihedral : 4.452 26.185 529 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.88 % Allowed : 17.63 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.43), residues: 425 helix: 1.99 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.13 (0.65), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 354 HIS 0.002 0.001 HIS A 49 PHE 0.010 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 42 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.304 Fit side-chains REVERT: A 435 MET cc_start: 0.7624 (tpp) cc_final: 0.7357 (tpp) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.7653 time to fit residues: 30.6411 Evaluate side-chains 38 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 408 MET 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: 0.7980 chunk 34 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1511 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= 0.188 Angle : 0.508 7.315 4494 Z= 0.253 Chirality : 0.037 0.125 536 Planarity : 0.004 0.041 551 Dihedral : 4.301 24.775 529 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 17.63 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.43), residues: 425 helix: 2.03 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.11 (0.66), 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 0.009 0.001 PHE A 44 TYR 0.011 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 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.338 Fit side-chains REVERT: A 420 MET cc_start: 0.8210 (mtp) cc_final: 0.7567 (mtt) REVERT: A 435 MET cc_start: 0.7609 (tpp) cc_final: 0.7340 (tpp) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.7761 time to fit residues: 29.4660 Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.0060 chunk 3 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.5314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1531 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= 0.208 Angle : 0.523 7.495 4494 Z= 0.259 Chirality : 0.037 0.132 536 Planarity : 0.004 0.041 551 Dihedral : 4.306 23.881 529 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.88 % Allowed : 17.63 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.43), residues: 425 helix: 2.02 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -0.14 (0.65), 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 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 ********************** 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 41 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.352 Fit side-chains REVERT: A 420 MET cc_start: 0.8207 (mtp) cc_final: 0.7536 (mtt) REVERT: A 435 MET cc_start: 0.7608 (tpp) cc_final: 0.7330 (tpp) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.7373 time to fit residues: 28.0283 Evaluate side-chains 40 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 400 VAL Chi-restraints excluded: chain A residue 408 MET 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: 1.9990 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.198330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.157649 restraints weight = 2945.476| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.61 r_work: 0.3520 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3283 Z= 0.255 Angle : 0.558 7.113 4494 Z= 0.277 Chirality : 0.038 0.141 536 Planarity : 0.004 0.041 551 Dihedral : 4.473 21.354 529 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.88 % Allowed : 17.95 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.43), residues: 425 helix: 1.96 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.09 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.003 0.001 HIS A 367 PHE 0.011 0.001 PHE A 44 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.98 seconds wall clock time: 25 minutes 10.53 seconds (1510.53 seconds total)