Starting phenix.real_space_refine on Wed Mar 5 22:59:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqo_60386/03_2025/8zqo_60386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqo_60386/03_2025/8zqo_60386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqo_60386/03_2025/8zqo_60386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqo_60386/03_2025/8zqo_60386.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqo_60386/03_2025/8zqo_60386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqo_60386/03_2025/8zqo_60386.cif" } resolution = 2.8 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= -0.001 sd= 0.063 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: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2683 2.51 5 N 607 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 4032 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3959 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CL': 1, ' NA': 2, 'HC6': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 2.98, per 1000 atoms: 0.74 Number of scatterers: 4032 At special positions: 0 Unit cell: (85, 75.65, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 20 16.00 Na 2 11.00 O 719 8.00 N 607 7.00 C 2683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 449.7 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.742A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.521A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.704A pdb=" N GLY A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.553A pdb=" N ALA A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.540A pdb=" N TRP A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.520A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 4.622A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 130 through 157 removed outlier: 4.301A pdb=" N ALA A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.602A pdb=" N TYR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.844A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix removed outlier: 3.601A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 262 removed outlier: 4.342A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 285 Processing helix chain 'A' and resid 285 through 297 removed outlier: 3.610A pdb=" N ILE A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.543A pdb=" N THR A 303 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.674A pdb=" N CYS A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 3.693A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 401 through 427 removed outlier: 4.159A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.546A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 478 through 504 removed outlier: 3.503A pdb=" N LEU A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 282 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.28 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: 601 1.31 - 1.43: 1178 1.43 - 1.56: 2328 1.56 - 1.68: 1 1.68 - 1.81: 35 Bond restraints: 4143 Sorted by residual: bond pdb=" C LEU A 97 " pdb=" O LEU A 97 " ideal model delta sigma weight residual 1.237 1.180 0.056 1.19e-02 7.06e+03 2.23e+01 bond pdb=" CA LEU A 97 " pdb=" C LEU A 97 " ideal model delta sigma weight residual 1.524 1.466 0.057 1.29e-02 6.01e+03 1.97e+01 bond pdb=" CAJ HC6 A 603 " pdb=" CAM HC6 A 603 " ideal model delta sigma weight residual 1.475 1.404 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N VAL A 402 " pdb=" CA VAL A 402 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.47e+00 bond pdb=" N GLN A 370 " pdb=" CA GLN A 370 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 6.86e+00 ... (remaining 4138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 5505 1.80 - 3.59: 112 3.59 - 5.39: 28 5.39 - 7.18: 11 7.18 - 8.98: 9 Bond angle restraints: 5665 Sorted by residual: angle pdb=" O ALA A 26 " pdb=" C ALA A 26 " pdb=" N TRP A 27 " ideal model delta sigma weight residual 122.12 118.41 3.71 1.06e+00 8.90e-01 1.22e+01 angle pdb=" CA ALA A 26 " pdb=" C ALA A 26 " pdb=" N TRP A 27 " ideal model delta sigma weight residual 117.30 120.98 -3.68 1.16e+00 7.43e-01 1.01e+01 angle pdb=" N VAL A 63 " pdb=" CA VAL A 63 " pdb=" C VAL A 63 " ideal model delta sigma weight residual 109.34 115.74 -6.40 2.08e+00 2.31e-01 9.47e+00 angle pdb=" O ILE A 96 " pdb=" C ILE A 96 " pdb=" N LEU A 97 " ideal model delta sigma weight residual 121.87 118.94 2.93 9.70e-01 1.06e+00 9.12e+00 angle pdb=" N GLY A 64 " pdb=" CA GLY A 64 " pdb=" C GLY A 64 " ideal model delta sigma weight residual 112.64 117.89 -5.25 1.74e+00 3.30e-01 9.10e+00 ... (remaining 5660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 2188 21.89 - 43.78: 172 43.78 - 65.67: 39 65.67 - 87.57: 10 87.57 - 109.46: 4 Dihedral angle restraints: 2413 sinusoidal: 932 harmonic: 1481 Sorted by residual: dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.25 109.46 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.85 107.47 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C6 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O4 BMA B 3 " ideal model delta sinusoidal sigma weight residual -163.34 -59.86 -103.48 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 2410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 596 0.070 - 0.140: 58 0.140 - 0.210: 4 0.210 - 0.280: 1 0.280 - 0.350: 1 Chirality restraints: 660 Sorted by residual: chirality pdb=" CAD HC6 A 603 " pdb=" CAC HC6 A 603 " pdb=" CAG HC6 A 603 " pdb=" OAE HC6 A 603 " both_signs ideal model delta sigma weight residual False 2.61 2.26 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LEU A 482 " pdb=" N LEU A 482 " pdb=" C LEU A 482 " pdb=" CB LEU A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 657 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ HC6 A 603 " -0.037 2.00e-02 2.50e+03 1.98e-02 7.83e+00 pdb=" CAM HC6 A 603 " 0.038 2.00e-02 2.50e+03 pdb=" CAN HC6 A 603 " 0.004 2.00e-02 2.50e+03 pdb=" CAO HC6 A 603 " 0.003 2.00e-02 2.50e+03 pdb=" CAP HC6 A 603 " -0.000 2.00e-02 2.50e+03 pdb=" CAQ HC6 A 603 " -0.002 2.00e-02 2.50e+03 pdb=" CAR HC6 A 603 " 0.009 2.00e-02 2.50e+03 pdb=" CAS HC6 A 603 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 457 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 458 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 452 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.027 5.00e-02 4.00e+02 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 82 2.70 - 3.25: 3911 3.25 - 3.80: 6225 3.80 - 4.35: 7865 4.35 - 4.90: 13854 Nonbonded interactions: 31937 Sorted by model distance: nonbonded pdb=" OD2 ASP A 188 " pdb="NA NA A 602 " model vdw 2.155 2.470 nonbonded pdb=" OG SER A 350 " pdb="NA NA A 602 " model vdw 2.173 2.470 nonbonded pdb=" OG SER A 346 " pdb="NA NA A 601 " model vdw 2.189 2.470 nonbonded pdb=" O VAL A 63 " pdb="NA NA A 601 " model vdw 2.232 2.470 nonbonded pdb=" OH TYR A 433 " pdb=" OD1 ASP A 512 " model vdw 2.236 3.040 ... (remaining 31932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.680 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.040 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:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 : 0.004 0.071 4143 Z= 0.301 Angle : 0.758 8.976 5665 Z= 0.392 Chirality : 0.046 0.350 660 Planarity : 0.006 0.071 683 Dihedral : 17.768 109.457 1477 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.20 % Allowed : 16.39 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.88 (0.39), residues: 513 helix: 1.82 (0.28), residues: 374 sheet: -3.68 (1.45), residues: 10 loop : 0.08 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.018 0.001 TYR A 175 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 1.1290 time to fit residues: 51.7760 Evaluate side-chains 36 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 373 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.096377 restraints weight = 4604.079| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.71 r_work: 0.2755 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4143 Z= 0.180 Angle : 0.582 8.038 5665 Z= 0.287 Chirality : 0.039 0.165 660 Planarity : 0.005 0.037 683 Dihedral : 11.845 74.030 657 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.41 % Allowed : 16.87 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.28 (0.39), residues: 513 helix: 2.17 (0.28), residues: 365 sheet: -3.75 (1.38), residues: 10 loop : 0.23 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 27 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 395 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (ttp) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 1.0659 time to fit residues: 47.9486 Evaluate side-chains 40 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095932 restraints weight = 4594.884| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.76 r_work: 0.2720 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4143 Z= 0.194 Angle : 0.574 8.039 5665 Z= 0.285 Chirality : 0.040 0.165 660 Planarity : 0.004 0.037 683 Dihedral : 9.723 63.307 654 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.65 % Allowed : 16.63 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.29 (0.39), residues: 513 helix: 2.15 (0.27), residues: 371 sheet: -3.78 (1.37), residues: 10 loop : 0.22 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 27 HIS 0.002 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7953 (t60) cc_final: 0.7316 (t-100) REVERT: A 395 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8222 (ttp) outliers start: 11 outliers final: 5 residues processed: 46 average time/residue: 1.0487 time to fit residues: 50.4897 Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097760 restraints weight = 4607.696| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.75 r_work: 0.2775 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4143 Z= 0.174 Angle : 0.546 8.281 5665 Z= 0.272 Chirality : 0.039 0.130 660 Planarity : 0.004 0.036 683 Dihedral : 8.614 60.004 654 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.17 % Allowed : 17.35 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.32 (0.39), residues: 513 helix: 2.18 (0.27), residues: 371 sheet: -3.74 (1.39), residues: 10 loop : 0.20 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.002 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.001 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7948 (t60) cc_final: 0.7314 (t-100) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 1.0637 time to fit residues: 47.8616 Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.0060 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.092474 restraints weight = 4577.515| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.75 r_work: 0.2809 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4143 Z= 0.159 Angle : 0.530 8.182 5665 Z= 0.264 Chirality : 0.038 0.118 660 Planarity : 0.004 0.036 683 Dihedral : 8.075 57.577 654 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.17 % Allowed : 17.35 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.39), residues: 513 helix: 2.25 (0.28), residues: 372 sheet: -3.66 (1.39), residues: 10 loop : 0.27 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7995 (t60) cc_final: 0.7375 (t-100) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 1.0864 time to fit residues: 47.6982 Evaluate side-chains 40 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.090418 restraints weight = 4473.692| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.73 r_work: 0.2749 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4143 Z= 0.192 Angle : 0.557 8.284 5665 Z= 0.279 Chirality : 0.039 0.136 660 Planarity : 0.004 0.038 683 Dihedral : 7.981 59.526 654 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.93 % Allowed : 17.83 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.29 (0.39), residues: 513 helix: 2.15 (0.27), residues: 371 sheet: -3.58 (1.41), residues: 10 loop : 0.19 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.018 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.8022 (t60) cc_final: 0.7382 (t-100) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 1.1125 time to fit residues: 47.6748 Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096400 restraints weight = 4675.968| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.77 r_work: 0.2757 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4143 Z= 0.162 Angle : 0.531 8.113 5665 Z= 0.265 Chirality : 0.038 0.118 660 Planarity : 0.004 0.036 683 Dihedral : 7.567 57.248 654 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.69 % Allowed : 17.59 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.39), residues: 513 helix: 2.24 (0.27), residues: 372 sheet: -3.56 (1.44), residues: 10 loop : 0.27 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.413 Fit side-chains REVERT: A 27 TRP cc_start: 0.7926 (t60) cc_final: 0.7263 (t-100) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 1.0978 time to fit residues: 45.8504 Evaluate side-chains 38 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.090101 restraints weight = 4479.608| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.76 r_work: 0.2720 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4143 Z= 0.197 Angle : 0.560 8.114 5665 Z= 0.282 Chirality : 0.039 0.139 660 Planarity : 0.004 0.039 683 Dihedral : 7.576 59.924 654 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.17 % Allowed : 17.35 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.24 (0.39), residues: 513 helix: 2.13 (0.27), residues: 371 sheet: -3.61 (1.41), residues: 10 loop : 0.13 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.018 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7976 (t60) cc_final: 0.7312 (t-100) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 1.1008 time to fit residues: 48.1958 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 0.0570 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102657 restraints weight = 4608.015| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.62 r_work: 0.2786 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4143 Z= 0.149 Angle : 0.517 8.013 5665 Z= 0.259 Chirality : 0.037 0.118 660 Planarity : 0.004 0.035 683 Dihedral : 7.046 55.851 654 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.45 % Allowed : 17.83 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.39), residues: 513 helix: 2.28 (0.27), residues: 372 sheet: -3.53 (1.45), residues: 10 loop : 0.21 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.440 Fit side-chains REVERT: A 27 TRP cc_start: 0.7975 (t60) cc_final: 0.7373 (t-100) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 1.0028 time to fit residues: 42.1877 Evaluate side-chains 38 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.0020 chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 overall best weight: 0.2426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104804 restraints weight = 4657.681| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.78 r_work: 0.2898 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4143 Z= 0.122 Angle : 0.470 7.784 5665 Z= 0.234 Chirality : 0.036 0.127 660 Planarity : 0.004 0.031 683 Dihedral : 6.067 59.458 654 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.72 % Allowed : 19.04 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.76 (0.39), residues: 513 helix: 2.45 (0.27), residues: 375 sheet: -3.55 (1.48), residues: 10 loop : 0.48 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 418 TYR 0.014 0.001 TYR A 175 ARG 0.004 0.000 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.560 Fit side-chains REVERT: A 314 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8052 (mp0) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 1.2180 time to fit residues: 49.8664 Evaluate side-chains 36 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 50 optimal weight: 0.4980 chunk 42 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101536 restraints weight = 4620.111| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.74 r_work: 0.2836 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4143 Z= 0.149 Angle : 0.502 8.095 5665 Z= 0.251 Chirality : 0.037 0.116 660 Planarity : 0.004 0.034 683 Dihedral : 6.379 57.944 654 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.72 % Allowed : 19.52 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.39), residues: 513 helix: 2.44 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.28 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.018 0.001 TYR A 67 ARG 0.004 0.001 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.91 seconds wall clock time: 56 minutes 19.30 seconds (3379.30 seconds total)