Starting phenix.real_space_refine on Wed Mar 5 17:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ju0_36658/03_2025/8ju0_36658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ju0_36658/03_2025/8ju0_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/cci-nas-00/data/ceres_data/8ju0_36658/03_2025/8ju0_36658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ju0_36658/03_2025/8ju0_36658.map" model { file = "/net/cci-nas-00/data/ceres_data/8ju0_36658/03_2025/8ju0_36658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ju0_36658/03_2025/8ju0_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. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.72, per 1000 atoms: 0.85 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 418.6 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: 0.32 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: 1.05 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: 0.00 - 3.48: 4455 3.48 - 6.96: 28 6.96 - 10.44: 8 10.44 - 13.91: 1 13.91 - 17.39: 2 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 3.040 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.240 3.040 nonbonded pdb=" O HIS A 367 " pdb=" OG1 THR A 371 " model vdw 2.246 3.040 nonbonded pdb=" O MET A 368 " pdb=" OG SER A 372 " model vdw 2.374 3.040 nonbonded pdb=" O ASN A 71 " pdb=" NH2 ARG A 113 " model vdw 2.375 3.120 ... (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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.650 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.331 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.5862 time to fit residues: 26.8634 Evaluate side-chains 33 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.201537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158895 restraints weight = 2969.814| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.72 r_work: 0.3513 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3283 Z= 0.260 Angle : 0.561 5.427 4494 Z= 0.283 Chirality : 0.038 0.130 536 Planarity : 0.004 0.047 551 Dihedral : 5.238 25.094 529 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 1.79 (0.42), residues: 425 helix: 1.69 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -0.12 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 260 PHE 0.010 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 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.334 Fit side-chains REVERT: A 447 GLN cc_start: 0.7435 (mm110) cc_final: 0.6986 (mm110) REVERT: A 448 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8200 (mpp) outliers start: 7 outliers final: 3 residues processed: 36 average time/residue: 0.7799 time to fit residues: 29.5699 Evaluate side-chains 35 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159749 restraints weight = 2951.540| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.64 r_work: 0.3520 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1220 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= 0.240 Angle : 0.537 6.051 4494 Z= 0.272 Chirality : 0.038 0.198 536 Planarity : 0.004 0.045 551 Dihedral : 5.015 27.070 529 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.60 % Allowed : 12.82 % 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: 1.77 (0.42), residues: 425 helix: 1.61 (0.30), residues: 319 sheet: None (None), residues: 0 loop : 0.00 (0.67), residues: 106 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 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.343 Fit side-chains REVERT: A 144 ASP cc_start: 0.7788 (m-30) cc_final: 0.7430 (m-30) REVERT: A 200 MET cc_start: 0.7589 (mmm) cc_final: 0.7245 (tpp) REVERT: A 420 MET cc_start: 0.8002 (mtp) cc_final: 0.7285 (mtt) REVERT: A 447 GLN cc_start: 0.7412 (mm110) cc_final: 0.7190 (mm110) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.8267 time to fit residues: 30.5167 Evaluate side-chains 34 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 40 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.200430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.159335 restraints weight = 3014.231| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.67 r_work: 0.3517 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1346 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= 0.231 Angle : 0.526 6.293 4494 Z= 0.266 Chirality : 0.038 0.162 536 Planarity : 0.004 0.044 551 Dihedral : 4.773 25.065 529 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.24 % Allowed : 14.42 % 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: 1.85 (0.43), residues: 425 helix: 1.66 (0.30), residues: 319 sheet: None (None), residues: 0 loop : 0.04 (0.66), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 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 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.307 Fit side-chains REVERT: A 144 ASP cc_start: 0.7792 (m-30) cc_final: 0.7439 (m-30) REVERT: A 200 MET cc_start: 0.7579 (mmm) cc_final: 0.7225 (tpp) REVERT: A 448 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8107 (mpp) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.7073 time to fit residues: 28.4236 Evaluate side-chains 37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 SER 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 509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.198523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157275 restraints weight = 2946.501| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.65 r_work: 0.3509 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1449 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= 0.247 Angle : 0.535 5.799 4494 Z= 0.271 Chirality : 0.038 0.140 536 Planarity : 0.004 0.043 551 Dihedral : 4.805 24.066 529 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.88 % Allowed : 14.74 % 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: 1.75 (0.42), residues: 425 helix: 1.61 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.12 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 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 to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.341 Fit side-chains REVERT: A 144 ASP cc_start: 0.7722 (m-30) cc_final: 0.7373 (m-30) REVERT: A 420 MET cc_start: 0.7938 (mtp) cc_final: 0.7241 (mtt) REVERT: A 447 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7215 (mm110) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 0.7018 time to fit residues: 29.6392 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 40 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.199296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.158088 restraints weight = 3066.308| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.69 r_work: 0.3522 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1478 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= 0.212 Angle : 0.518 6.306 4494 Z= 0.263 Chirality : 0.038 0.135 536 Planarity : 0.004 0.042 551 Dihedral : 4.682 24.041 529 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.21 % Allowed : 14.42 % 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: 1.83 (0.42), residues: 425 helix: 1.67 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.12 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.002 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 to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.386 Fit side-chains REVERT: A 144 ASP cc_start: 0.7716 (m-30) cc_final: 0.7370 (m-30) REVERT: A 435 MET cc_start: 0.7392 (tpp) cc_final: 0.7132 (tpp) REVERT: A 447 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7210 (mm110) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.6734 time to fit residues: 30.0021 Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 400 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.199361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.159269 restraints weight = 2946.921| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.59 r_work: 0.3519 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1563 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= 0.242 Angle : 0.533 6.568 4494 Z= 0.270 Chirality : 0.038 0.130 536 Planarity : 0.004 0.041 551 Dihedral : 4.716 23.798 529 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.53 % Allowed : 14.42 % 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: 1.78 (0.42), residues: 425 helix: 1.64 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.12 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.003 0.001 HIS A 367 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 to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.310 Fit side-chains REVERT: A 447 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7211 (mm110) outliers start: 11 outliers final: 8 residues processed: 41 average time/residue: 0.6532 time to fit residues: 28.3882 Evaluate side-chains 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.199727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159105 restraints weight = 2984.359| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.65 r_work: 0.3536 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1555 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 : 0.527 6.924 4494 Z= 0.267 Chirality : 0.038 0.130 536 Planarity : 0.004 0.041 551 Dihedral : 4.615 23.432 529 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.88 % Allowed : 14.74 % 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: 1.85 (0.43), residues: 425 helix: 1.70 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.13 (0.67), residues: 104 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 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 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.339 Fit side-chains REVERT: A 435 MET cc_start: 0.7461 (tpp) cc_final: 0.7197 (tpp) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.7037 time to fit residues: 28.2541 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 400 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.0010 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.202383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162319 restraints weight = 3041.655| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.65 r_work: 0.3559 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.1567 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= 0.184 Angle : 0.510 7.202 4494 Z= 0.258 Chirality : 0.037 0.134 536 Planarity : 0.004 0.041 551 Dihedral : 4.469 23.280 529 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.21 % Allowed : 15.06 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.43), residues: 425 helix: 1.78 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.08 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 367 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 to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.326 Fit side-chains REVERT: A 420 MET cc_start: 0.7929 (mtp) cc_final: 0.7300 (mtt) REVERT: A 435 MET cc_start: 0.7384 (tpp) cc_final: 0.7112 (tpp) outliers start: 10 outliers final: 8 residues processed: 36 average time/residue: 0.7028 time to fit residues: 26.7877 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP 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 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 15 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.198512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157833 restraints weight = 2944.249| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.66 r_work: 0.3521 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1630 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= 0.245 Angle : 0.547 7.326 4494 Z= 0.275 Chirality : 0.039 0.139 536 Planarity : 0.004 0.041 551 Dihedral : 4.614 23.061 529 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 1.82 (0.43), residues: 425 helix: 1.67 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.11 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 354 HIS 0.002 0.001 HIS A 367 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 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.337 Fit side-chains REVERT: A 435 MET cc_start: 0.7508 (tpp) cc_final: 0.7227 (tpp) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.7087 time to fit residues: 26.9665 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP 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 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 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 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 = 0.4144 r_free = 0.4144 target = 0.197961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150245 restraints weight = 2922.913| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.87 r_work: 0.3531 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1687 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= 0.258 Angle : 0.551 7.256 4494 Z= 0.278 Chirality : 0.039 0.144 536 Planarity : 0.004 0.041 551 Dihedral : 4.707 20.143 529 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.21 % Allowed : 15.38 % 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: 1.77 (0.43), residues: 425 helix: 1.63 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.16 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 367 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.05 seconds wall clock time: 46 minutes 50.45 seconds (2810.45 seconds total)