Starting phenix.real_space_refine on Wed Mar 5 21:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjh_37580/03_2025/8wjh_37580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjh_37580/03_2025/8wjh_37580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjh_37580/03_2025/8wjh_37580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjh_37580/03_2025/8wjh_37580.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjh_37580/03_2025/8wjh_37580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjh_37580/03_2025/8wjh_37580.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 Cl 1 4.86 5 C 2493 2.51 5 N 643 2.21 5 O 658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3823 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 478} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.00, per 1000 atoms: 0.78 Number of scatterers: 3824 At special positions: 0 Unit cell: (90.95, 77.04, 88.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 29 16.00 O 658 8.00 N 643 7.00 C 2493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.04 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " 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: 1.26 Conformation dependent library (CDL) restraints added in 506.8 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 82.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 3.618A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 36 removed outlier: 3.601A pdb=" N THR A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Proline residue: A 27 - end of helix Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 140 through 164 Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.522A pdb=" N MET A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 192 through 222 Processing helix chain 'A' and resid 223 through 253 removed outlier: 4.552A pdb=" N ALA A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 276 Proline residue: A 265 - end of helix removed outlier: 3.880A pdb=" N LEU A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 303 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 400 through 422 Processing helix chain 'A' and resid 426 through 456 removed outlier: 3.716A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 484 removed outlier: 3.556A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 491 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 removed outlier: 4.036A pdb=" N ARG A 87 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 111 " --> pdb=" O ARG A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 289 hydrogen bonds defined for protein. 858 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: 1.04 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1191 1.35 - 1.47: 985 1.47 - 1.60: 1692 1.60 - 1.72: 0 1.72 - 1.85: 45 Bond restraints: 3913 Sorted by residual: bond pdb=" N ARG A 473 " pdb=" CA ARG A 473 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.23e-02 6.61e+03 6.14e+00 bond pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.34e+00 bond pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.88e+00 bond pdb=" CA LEU A 26 " pdb=" C LEU A 26 " ideal model delta sigma weight residual 1.521 1.543 -0.021 1.11e-02 8.12e+03 3.69e+00 bond pdb=" C VAL A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.10e+00 ... (remaining 3908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 5118 2.87 - 5.75: 170 5.75 - 8.62: 29 8.62 - 11.50: 6 11.50 - 14.37: 4 Bond angle restraints: 5327 Sorted by residual: angle pdb=" C CYS A 136 " pdb=" CA CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sigma weight residual 110.42 124.79 -14.37 1.99e+00 2.53e-01 5.22e+01 angle pdb=" C VAL A 135 " pdb=" N CYS A 136 " pdb=" CA CYS A 136 " ideal model delta sigma weight residual 121.54 133.18 -11.64 1.91e+00 2.74e-01 3.71e+01 angle pdb=" N VAL A 460 " pdb=" CA VAL A 460 " pdb=" C VAL A 460 " ideal model delta sigma weight residual 113.43 107.42 6.01 1.09e+00 8.42e-01 3.04e+01 angle pdb=" C ALA A 390 " pdb=" N THR A 391 " pdb=" CA THR A 391 " ideal model delta sigma weight residual 121.14 112.79 8.35 1.75e+00 3.27e-01 2.27e+01 angle pdb=" N THR A 392 " pdb=" CA THR A 392 " pdb=" C THR A 392 " ideal model delta sigma weight residual 111.28 106.36 4.92 1.09e+00 8.42e-01 2.04e+01 ... (remaining 5322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2080 17.34 - 34.68: 149 34.68 - 52.02: 49 52.02 - 69.36: 19 69.36 - 86.70: 8 Dihedral angle restraints: 2305 sinusoidal: 864 harmonic: 1441 Sorted by residual: dihedral pdb=" CB CYS A 85 " pdb=" SG CYS A 85 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 11.55 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 113 " pdb=" CB CYS A 113 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" C CYS A 136 " pdb=" N CYS A 136 " pdb=" CA CYS A 136 " pdb=" CB CYS A 136 " ideal model delta harmonic sigma weight residual -122.60 -140.65 18.05 0 2.50e+00 1.60e-01 5.21e+01 ... (remaining 2302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 578 0.116 - 0.232: 47 0.232 - 0.349: 1 0.349 - 0.465: 1 0.465 - 0.581: 2 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA CYS A 136 " pdb=" N CYS A 136 " pdb=" C CYS A 136 " pdb=" CB CYS A 136 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CG LEU A 296 " pdb=" CB LEU A 296 " pdb=" CD1 LEU A 296 " pdb=" CD2 LEU A 296 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE A 269 " pdb=" CA ILE A 269 " pdb=" CG1 ILE A 269 " pdb=" CG2 ILE A 269 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 626 not shown) Planarity restraints: 662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 459 " -0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C PRO A 459 " 0.084 2.00e-02 2.50e+03 pdb=" O PRO A 459 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL A 460 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 390 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C ALA A 390 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 390 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 391 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 94 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLN A 94 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN A 94 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 659 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 754 2.78 - 3.31: 3894 3.31 - 3.84: 6500 3.84 - 4.37: 7086 4.37 - 4.90: 12471 Nonbonded interactions: 30705 Sorted by model distance: nonbonded pdb=" OD1 ASP A 366 " pdb=" NH2 ARG A 486 " model vdw 2.256 3.120 nonbonded pdb=" O MET A 218 " pdb=" OG1 THR A 222 " model vdw 2.306 3.040 nonbonded pdb=" O GLN A 424 " pdb=" NE2 GLN A 427 " model vdw 2.344 3.120 nonbonded pdb=" O LEU A 212 " pdb=" OG1 THR A 216 " model vdw 2.374 3.040 nonbonded pdb=" NH2 ARG A 89 " pdb=" O ALA A 108 " model vdw 2.383 3.120 ... (remaining 30700 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 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 0.070 3913 Z= 0.399 Angle : 1.268 14.373 5327 Z= 0.719 Chirality : 0.069 0.581 629 Planarity : 0.009 0.064 662 Dihedral : 15.606 86.704 1367 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.00 % Allowed : 19.75 % Favored : 79.25 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.35), residues: 499 helix: 0.78 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -0.42 (0.55), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 282 HIS 0.003 0.001 HIS A 47 PHE 0.031 0.003 PHE A 354 TYR 0.021 0.005 TYR A 119 ARG 0.017 0.003 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.402 Fit side-chains REVERT: A 473 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6036 (mtp180) outliers start: 4 outliers final: 0 residues processed: 33 average time/residue: 0.1471 time to fit residues: 6.5819 Evaluate side-chains 30 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN 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 = 0.194999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139062 restraints weight = 3746.910| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.23 r_work: 0.3483 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3913 Z= 0.236 Angle : 0.639 6.687 5327 Z= 0.328 Chirality : 0.041 0.181 629 Planarity : 0.004 0.030 662 Dihedral : 5.358 58.055 538 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.00 % Allowed : 17.50 % Favored : 80.50 % 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 (0.38), residues: 499 helix: 1.67 (0.27), residues: 375 sheet: -0.40 (1.51), residues: 10 loop : -0.17 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.018 0.002 PHE A 267 TYR 0.011 0.002 TYR A 361 ARG 0.003 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.458 Fit side-chains REVERT: A 473 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6672 (mtt180) outliers start: 8 outliers final: 3 residues processed: 35 average time/residue: 0.1372 time to fit residues: 6.6580 Evaluate side-chains 32 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 473 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.189606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134234 restraints weight = 3781.759| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.21 r_work: 0.3403 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3913 Z= 0.236 Angle : 0.617 10.784 5327 Z= 0.307 Chirality : 0.040 0.163 629 Planarity : 0.004 0.035 662 Dihedral : 4.977 52.057 538 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.75 % Allowed : 17.75 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.38), residues: 499 helix: 1.38 (0.27), residues: 390 sheet: -1.01 (1.45), residues: 10 loop : 0.15 (0.66), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 282 HIS 0.001 0.000 HIS A 305 PHE 0.016 0.002 PHE A 205 TYR 0.010 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4904 (mtp) cc_final: 0.3748 (pmm) REVERT: A 136 CYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6993 (t) REVERT: A 411 MET cc_start: 0.6299 (mmp) cc_final: 0.6053 (tpp) REVERT: A 482 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7014 (tp) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.1139 time to fit residues: 6.5523 Evaluate side-chains 34 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 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 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.189049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132847 restraints weight = 3777.949| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.25 r_work: 0.3389 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3913 Z= 0.211 Angle : 0.553 6.462 5327 Z= 0.278 Chirality : 0.038 0.160 629 Planarity : 0.004 0.037 662 Dihedral : 3.964 17.661 534 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.00 % Allowed : 19.25 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.38), residues: 499 helix: 1.36 (0.27), residues: 390 sheet: -1.24 (1.45), residues: 10 loop : 0.21 (0.66), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 282 HIS 0.001 0.000 HIS A 52 PHE 0.014 0.001 PHE A 205 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4820 (mtp) cc_final: 0.3636 (pmm) REVERT: A 136 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.7106 (t) REVERT: A 411 MET cc_start: 0.6494 (mmp) cc_final: 0.6192 (tpp) outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.1185 time to fit residues: 5.9084 Evaluate side-chains 31 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.194611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136319 restraints weight = 3841.079| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.41 r_work: 0.3242 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3913 Z= 0.203 Angle : 0.551 7.020 5327 Z= 0.274 Chirality : 0.038 0.144 629 Planarity : 0.004 0.037 662 Dihedral : 3.851 16.782 534 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.25 % Allowed : 21.25 % Favored : 76.50 % 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 (0.39), residues: 499 helix: 1.45 (0.27), residues: 388 sheet: None (None), residues: 0 loop : 0.48 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 282 HIS 0.001 0.000 HIS A 305 PHE 0.013 0.001 PHE A 205 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4683 (mtp) cc_final: 0.3525 (pmm) REVERT: A 136 CYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7157 (t) REVERT: A 231 MET cc_start: 0.6059 (mmp) cc_final: 0.5827 (mmp) REVERT: A 317 MET cc_start: 0.5136 (pmm) cc_final: 0.4651 (ppp) REVERT: A 411 MET cc_start: 0.6116 (mmp) cc_final: 0.5829 (tpp) REVERT: A 482 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6713 (tp) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.1179 time to fit residues: 6.0226 Evaluate side-chains 33 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 482 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.184042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125101 restraints weight = 3885.822| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.46 r_work: 0.3167 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3913 Z= 0.367 Angle : 0.636 7.190 5327 Z= 0.320 Chirality : 0.042 0.144 629 Planarity : 0.005 0.037 662 Dihedral : 4.161 20.745 534 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.25 % Allowed : 21.00 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.38), residues: 499 helix: 1.34 (0.27), residues: 363 sheet: None (None), residues: 0 loop : 0.10 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.001 HIS A 52 PHE 0.015 0.002 PHE A 205 TYR 0.010 0.002 TYR A 361 ARG 0.003 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4917 (mtp) cc_final: 0.3643 (pmm) REVERT: A 24 PHE cc_start: 0.7192 (m-80) cc_final: 0.6804 (m-80) REVERT: A 211 PHE cc_start: 0.6499 (m-10) cc_final: 0.6093 (m-80) REVERT: A 317 MET cc_start: 0.5298 (pmm) cc_final: 0.4793 (ppp) REVERT: A 411 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5687 (tpp) outliers start: 13 outliers final: 8 residues processed: 42 average time/residue: 0.1481 time to fit residues: 8.1585 Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 411 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.189249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131001 restraints weight = 3747.579| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.39 r_work: 0.3221 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3913 Z= 0.204 Angle : 0.547 6.521 5327 Z= 0.273 Chirality : 0.038 0.139 629 Planarity : 0.004 0.035 662 Dihedral : 3.982 19.210 534 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.00 % Allowed : 21.75 % Favored : 75.25 % 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 (0.39), residues: 499 helix: 1.57 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.25 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 52 PHE 0.013 0.001 PHE A 205 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4858 (mtp) cc_final: 0.3589 (pmm) REVERT: A 231 MET cc_start: 0.6147 (mmp) cc_final: 0.5869 (mmp) REVERT: A 317 MET cc_start: 0.5561 (pmm) cc_final: 0.5114 (ppp) REVERT: A 411 MET cc_start: 0.6190 (mmt) cc_final: 0.5906 (tpp) outliers start: 12 outliers final: 6 residues processed: 40 average time/residue: 0.1094 time to fit residues: 6.3350 Evaluate side-chains 32 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.192347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135091 restraints weight = 3753.747| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.35 r_work: 0.3261 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3913 Z= 0.196 Angle : 0.542 6.632 5327 Z= 0.269 Chirality : 0.038 0.135 629 Planarity : 0.004 0.035 662 Dihedral : 3.893 15.986 534 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.75 % Allowed : 21.75 % Favored : 75.50 % 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: 1.90 (0.39), residues: 499 helix: 1.67 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.23 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.001 0.000 HIS A 305 PHE 0.012 0.001 PHE A 354 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4874 (mtp) cc_final: 0.3582 (pmm) REVERT: A 107 GLU cc_start: 0.4531 (OUTLIER) cc_final: 0.4271 (tp30) REVERT: A 231 MET cc_start: 0.6145 (mmp) cc_final: 0.5872 (mmp) REVERT: A 317 MET cc_start: 0.5515 (pmm) cc_final: 0.4982 (ppp) REVERT: A 411 MET cc_start: 0.6208 (mmt) cc_final: 0.5923 (tpp) REVERT: A 482 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6755 (tp) outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.1137 time to fit residues: 6.2044 Evaluate side-chains 37 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 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 = 0.4122 r_free = 0.4122 target = 0.189424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132519 restraints weight = 3718.984| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.32 r_work: 0.3261 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3913 Z= 0.192 Angle : 0.537 6.579 5327 Z= 0.267 Chirality : 0.037 0.131 629 Planarity : 0.004 0.035 662 Dihedral : 3.855 15.333 534 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.50 % Allowed : 21.75 % Favored : 75.75 % 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: 1.93 (0.39), residues: 499 helix: 1.70 (0.27), residues: 369 sheet: None (None), residues: 0 loop : 0.21 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.013 0.001 PHE A 205 TYR 0.009 0.001 TYR A 361 ARG 0.005 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4790 (mtp) cc_final: 0.3539 (pmm) REVERT: A 107 GLU cc_start: 0.4386 (OUTLIER) cc_final: 0.4012 (tp30) REVERT: A 317 MET cc_start: 0.5482 (pmm) cc_final: 0.4986 (ppp) REVERT: A 411 MET cc_start: 0.6135 (mmt) cc_final: 0.5853 (tpp) REVERT: A 482 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6702 (tp) outliers start: 10 outliers final: 8 residues processed: 36 average time/residue: 0.1134 time to fit residues: 5.8360 Evaluate side-chains 36 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 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 = 0.4127 r_free = 0.4127 target = 0.190005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132902 restraints weight = 3759.819| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.34 r_work: 0.3265 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3913 Z= 0.189 Angle : 0.532 6.563 5327 Z= 0.263 Chirality : 0.037 0.129 629 Planarity : 0.004 0.035 662 Dihedral : 3.796 14.808 534 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.25 % Allowed : 22.00 % Favored : 75.75 % 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 (0.39), residues: 499 helix: 1.70 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.28 (0.62), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 354 TYR 0.009 0.001 TYR A 361 ARG 0.005 0.000 ARG A 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4826 (mtp) cc_final: 0.3558 (pmm) REVERT: A 28 CYS cc_start: 0.7591 (m) cc_final: 0.7108 (p) REVERT: A 317 MET cc_start: 0.5384 (pmm) cc_final: 0.4882 (ppp) REVERT: A 411 MET cc_start: 0.6238 (mmt) cc_final: 0.5952 (tpp) REVERT: A 482 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6662 (tp) outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1176 time to fit residues: 5.9292 Evaluate side-chains 33 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 32 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.193959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136125 restraints weight = 3757.699| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.36 r_work: 0.3263 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3913 Z= 0.191 Angle : 0.532 6.603 5327 Z= 0.263 Chirality : 0.037 0.129 629 Planarity : 0.004 0.035 662 Dihedral : 3.773 14.650 534 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.50 % Allowed : 21.50 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.39), residues: 499 helix: 1.71 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.29 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.001 0.000 HIS A 47 PHE 0.011 0.001 PHE A 354 TYR 0.009 0.001 TYR A 361 ARG 0.004 0.000 ARG A 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2429.67 seconds wall clock time: 42 minutes 31.28 seconds (2551.28 seconds total)