Starting phenix.real_space_refine on Wed Jun 4 22:48:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfg_34720/06_2025/8hfg_34720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfg_34720/06_2025/8hfg_34720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfg_34720/06_2025/8hfg_34720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfg_34720/06_2025/8hfg_34720.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfg_34720/06_2025/8hfg_34720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfg_34720/06_2025/8hfg_34720.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.168 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 20 5.16 5 Cl 1 4.86 5 C 2950 2.51 5 N 679 2.21 5 O 744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4394 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4366 Classifications: {'peptide': 545} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 525} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 28 Unusual residues: {' CL': 1, 'LDP': 2} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Time building chain proxies: 3.00, per 1000 atoms: 0.68 Number of scatterers: 4394 At special positions: 0 Unit cell: (71.445, 68.1975, 96.3425, 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 20 16.00 O 744 8.00 N 679 7.00 C 2950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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: 1.05 Conformation dependent library (CDL) restraints added in 484.8 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.687A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.594A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 4.016A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.623A pdb=" N LEU A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.521A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.073A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.803A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.714A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.787A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.704A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.731A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.848A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.646A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.810A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 289 hydrogen bonds defined for protein. 843 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: 1.12 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 644 1.26 - 1.40: 1311 1.40 - 1.54: 2448 1.54 - 1.68: 96 1.68 - 1.81: 31 Bond restraints: 4530 Sorted by residual: bond pdb=" C LEU A 302 " pdb=" O LEU A 302 " ideal model delta sigma weight residual 1.236 1.121 0.115 1.31e-02 5.83e+03 7.71e+01 bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.134 0.100 1.35e-02 5.49e+03 5.53e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.47e-02 4.63e+03 3.82e+01 bond pdb=" C ARG A 301 " pdb=" O ARG A 301 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.32e-02 5.74e+03 3.38e+01 bond pdb=" C LYS A 88 " pdb=" O LYS A 88 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.16e-02 7.43e+03 3.33e+01 ... (remaining 4525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 6105 3.24 - 6.49: 59 6.49 - 9.73: 9 9.73 - 12.97: 3 12.97 - 16.22: 2 Bond angle restraints: 6178 Sorted by residual: angle pdb=" N LEU A 302 " pdb=" CA LEU A 302 " pdb=" C LEU A 302 " ideal model delta sigma weight residual 113.18 99.01 14.17 1.21e+00 6.83e-01 1.37e+02 angle pdb=" N TYR A 300 " pdb=" CA TYR A 300 " pdb=" C TYR A 300 " ideal model delta sigma weight residual 113.28 101.21 12.07 1.22e+00 6.72e-01 9.78e+01 angle pdb=" C ARG A 301 " pdb=" CA ARG A 301 " pdb=" CB ARG A 301 " ideal model delta sigma weight residual 109.55 93.33 16.22 1.68e+00 3.54e-01 9.32e+01 angle pdb=" CA PRO A 83 " pdb=" N PRO A 83 " pdb=" CD PRO A 83 " ideal model delta sigma weight residual 112.00 99.50 12.50 1.40e+00 5.10e-01 7.98e+01 angle pdb=" O TYR A 87 " pdb=" C TYR A 87 " pdb=" N LYS A 88 " ideal model delta sigma weight residual 122.09 113.75 8.34 1.08e+00 8.57e-01 5.97e+01 ... (remaining 6173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 2205 17.29 - 34.57: 237 34.57 - 51.86: 59 51.86 - 69.15: 16 69.15 - 86.44: 4 Dihedral angle restraints: 2521 sinusoidal: 945 harmonic: 1576 Sorted by residual: dihedral pdb=" C ARG A 301 " pdb=" N ARG A 301 " pdb=" CA ARG A 301 " pdb=" CB ARG A 301 " ideal model delta harmonic sigma weight residual -122.60 -103.73 -18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual 180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -133.40 10.80 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 2518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 670 0.095 - 0.189: 14 0.189 - 0.284: 2 0.284 - 0.379: 0 0.379 - 0.474: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA LYS A 88 " pdb=" N LYS A 88 " pdb=" C LYS A 88 " pdb=" CB LYS A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE A 617 " pdb=" N ILE A 617 " pdb=" C ILE A 617 " pdb=" CB ILE A 617 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 684 not shown) Planarity restraints: 749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 93 " 0.026 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C ALA A 93 " -0.092 2.00e-02 2.50e+03 pdb=" O ALA A 93 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE A 94 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " 0.086 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO A 83 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 ... (remaining 746 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 48 2.63 - 3.20: 4094 3.20 - 3.77: 6981 3.77 - 4.33: 9779 4.33 - 4.90: 16616 Nonbonded interactions: 37518 Sorted by model distance: nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 803 " model vdw 2.067 3.040 nonbonded pdb=" O PHE A 577 " pdb=" NH1 ARG A 587 " model vdw 2.146 3.120 nonbonded pdb=" O2 LDP A 701 " pdb=" O HOH A 801 " model vdw 2.253 3.040 nonbonded pdb=" NH1 ARG A 121 " pdb=" O ASN A 333 " model vdw 2.308 3.120 nonbonded pdb=" O GLY A 90 " pdb=" O HOH A 802 " model vdw 2.318 3.040 ... (remaining 37513 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 0.131 4531 Z= 0.392 Angle : 0.804 16.218 6180 Z= 0.503 Chirality : 0.043 0.474 687 Planarity : 0.007 0.122 749 Dihedral : 15.709 86.436 1514 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.15 % Favored : 96.66 % Rotamer: Outliers : 1.96 % Allowed : 15.43 % Favored : 82.61 % Cbeta Deviations : 0.60 % 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: 1.59 (0.38), residues: 539 helix: 1.74 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.33 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.006 0.001 HIS A 296 PHE 0.021 0.001 PHE A 299 TYR 0.019 0.001 TYR A 300 ARG 0.002 0.000 ARG A 512 Details of bonding type rmsd hydrogen bonds : bond 0.11866 ( 289) hydrogen bonds : angle 5.11628 ( 843) SS BOND : bond 0.00181 ( 1) SS BOND : angle 1.24496 ( 2) covalent geometry : bond 0.00611 ( 4530) covalent geometry : angle 0.80407 ( 6178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.408 Fit side-chains REVERT: A 300 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.5277 (m-10) outliers start: 9 outliers final: 2 residues processed: 86 average time/residue: 0.8125 time to fit residues: 73.6778 Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134284 restraints weight = 4596.461| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.42 r_work: 0.3408 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4531 Z= 0.187 Angle : 0.632 7.739 6180 Z= 0.327 Chirality : 0.042 0.147 687 Planarity : 0.005 0.064 749 Dihedral : 6.278 71.975 595 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.91 % Allowed : 17.83 % Favored : 78.26 % 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: 1.29 (0.37), residues: 539 helix: 1.32 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.08 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 235 HIS 0.005 0.001 HIS A 199 PHE 0.021 0.002 PHE A 94 TYR 0.017 0.002 TYR A 84 ARG 0.004 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 289) hydrogen bonds : angle 4.98718 ( 843) SS BOND : bond 0.01038 ( 1) SS BOND : angle 0.69220 ( 2) covalent geometry : bond 0.00419 ( 4530) covalent geometry : angle 0.63188 ( 6178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.460 Fit side-chains REVERT: A 296 HIS cc_start: 0.7072 (t70) cc_final: 0.6809 (t70) REVERT: A 373 LYS cc_start: 0.7632 (mmmm) cc_final: 0.7171 (mmpt) REVERT: A 375 ASN cc_start: 0.7640 (m-40) cc_final: 0.7138 (t0) REVERT: A 377 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 403 PHE cc_start: 0.7230 (t80) cc_final: 0.7011 (t80) REVERT: A 425 GLU cc_start: 0.8640 (tp30) cc_final: 0.8407 (mm-30) REVERT: A 500 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6533 (ttp-170) REVERT: A 507 GLN cc_start: 0.8074 (tt0) cc_final: 0.7622 (tt0) REVERT: A 556 TRP cc_start: 0.7301 (m100) cc_final: 0.5970 (m-10) REVERT: A 595 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7172 (mt-10) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 0.6978 time to fit residues: 61.6591 Evaluate side-chains 70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128594 restraints weight = 4629.921| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.78 r_work: 0.3329 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4531 Z= 0.170 Angle : 0.579 8.075 6180 Z= 0.290 Chirality : 0.041 0.152 687 Planarity : 0.005 0.051 749 Dihedral : 5.531 66.578 592 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.00 % Allowed : 17.83 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.37), residues: 539 helix: 1.46 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.07 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.004 0.001 HIS A 599 PHE 0.016 0.002 PHE A 110 TYR 0.021 0.002 TYR A 84 ARG 0.004 0.001 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 289) hydrogen bonds : angle 4.89264 ( 843) SS BOND : bond 0.00792 ( 1) SS BOND : angle 1.96218 ( 2) covalent geometry : bond 0.00416 ( 4530) covalent geometry : angle 0.57797 ( 6178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.478 Fit side-chains REVERT: A 310 ASP cc_start: 0.7943 (m-30) cc_final: 0.7677 (m-30) REVERT: A 373 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7387 (mtmt) REVERT: A 403 PHE cc_start: 0.7768 (t80) cc_final: 0.7535 (t80) REVERT: A 431 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7681 (mt) REVERT: A 500 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6837 (ttp-170) REVERT: A 507 GLN cc_start: 0.8119 (tt0) cc_final: 0.7618 (tt0) REVERT: A 556 TRP cc_start: 0.7787 (m100) cc_final: 0.6386 (m-10) REVERT: A 595 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7411 (mt-10) outliers start: 23 outliers final: 7 residues processed: 76 average time/residue: 0.6779 time to fit residues: 54.9896 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 595 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.154429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128450 restraints weight = 4653.582| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.65 r_work: 0.3327 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4531 Z= 0.159 Angle : 0.561 7.282 6180 Z= 0.282 Chirality : 0.041 0.160 687 Planarity : 0.005 0.049 749 Dihedral : 5.249 57.379 590 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.91 % Allowed : 19.35 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.37), residues: 539 helix: 1.55 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.04 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 PHE 0.028 0.002 PHE A 408 TYR 0.021 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 289) hydrogen bonds : angle 4.90891 ( 843) SS BOND : bond 0.00055 ( 1) SS BOND : angle 1.28532 ( 2) covalent geometry : bond 0.00393 ( 4530) covalent geometry : angle 0.56019 ( 6178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.437 Fit side-chains REVERT: A 373 LYS cc_start: 0.8242 (mmmm) cc_final: 0.7669 (mtmt) REVERT: A 500 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6950 (ttp-170) REVERT: A 507 GLN cc_start: 0.8196 (tt0) cc_final: 0.7674 (tt0) REVERT: A 588 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7328 (mm) REVERT: A 595 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7499 (mt-10) outliers start: 18 outliers final: 9 residues processed: 66 average time/residue: 0.7653 time to fit residues: 53.5425 Evaluate side-chains 63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 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 = 0.3492 r_free = 0.3492 target = 0.141161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119682 restraints weight = 4926.964| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.20 r_work: 0.3154 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4531 Z= 0.142 Angle : 0.529 7.004 6180 Z= 0.267 Chirality : 0.039 0.169 687 Planarity : 0.004 0.047 749 Dihedral : 4.969 48.950 590 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.26 % Allowed : 19.78 % Favored : 76.96 % 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: 1.66 (0.37), residues: 539 helix: 1.61 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.01 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 PHE 0.014 0.001 PHE A 110 TYR 0.020 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 289) hydrogen bonds : angle 4.86670 ( 843) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.99112 ( 2) covalent geometry : bond 0.00349 ( 4530) covalent geometry : angle 0.52892 ( 6178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 500 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7315 (ttp-170) REVERT: A 507 GLN cc_start: 0.8342 (tt0) cc_final: 0.7882 (tt0) REVERT: A 595 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7577 (mt-10) outliers start: 15 outliers final: 7 residues processed: 64 average time/residue: 0.6643 time to fit residues: 45.5098 Evaluate side-chains 61 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.140878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119529 restraints weight = 4691.061| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.21 r_work: 0.3164 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4531 Z= 0.128 Angle : 0.523 8.065 6180 Z= 0.260 Chirality : 0.039 0.185 687 Planarity : 0.004 0.046 749 Dihedral : 4.802 44.832 590 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.70 % Allowed : 19.35 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.37), residues: 539 helix: 1.66 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.12 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 PHE 0.047 0.001 PHE A 408 TYR 0.019 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 289) hydrogen bonds : angle 4.78466 ( 843) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.99528 ( 2) covalent geometry : bond 0.00306 ( 4530) covalent geometry : angle 0.52282 ( 6178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 174 THR cc_start: 0.8427 (m) cc_final: 0.7977 (p) REVERT: A 418 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: A 500 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7193 (ttp-170) REVERT: A 507 GLN cc_start: 0.8324 (tt0) cc_final: 0.7867 (tt0) REVERT: A 595 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7523 (mt-10) outliers start: 17 outliers final: 9 residues processed: 68 average time/residue: 0.9778 time to fit residues: 70.7437 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.141317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.120036 restraints weight = 4809.709| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.19 r_work: 0.3149 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.7626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4531 Z= 0.137 Angle : 0.541 7.778 6180 Z= 0.268 Chirality : 0.039 0.166 687 Planarity : 0.004 0.045 749 Dihedral : 4.668 44.018 590 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.83 % Allowed : 20.87 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.37), residues: 539 helix: 1.63 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.20 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 404 HIS 0.003 0.001 HIS A 599 PHE 0.040 0.001 PHE A 408 TYR 0.020 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 289) hydrogen bonds : angle 4.82835 ( 843) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.96635 ( 2) covalent geometry : bond 0.00334 ( 4530) covalent geometry : angle 0.54049 ( 6178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 174 THR cc_start: 0.8531 (m) cc_final: 0.8091 (p) REVERT: A 403 PHE cc_start: 0.8164 (t80) cc_final: 0.7872 (t80) REVERT: A 418 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: A 500 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7308 (ttp-170) REVERT: A 507 GLN cc_start: 0.8339 (tt0) cc_final: 0.7911 (tt0) REVERT: A 588 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 595 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7608 (mt-10) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.7502 time to fit residues: 52.8813 Evaluate side-chains 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.142152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.119831 restraints weight = 4807.184| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.20 r_work: 0.3159 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4531 Z= 0.129 Angle : 0.531 7.516 6180 Z= 0.263 Chirality : 0.039 0.192 687 Planarity : 0.004 0.044 749 Dihedral : 4.591 45.926 590 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.83 % Allowed : 20.43 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.37), residues: 539 helix: 1.65 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.32 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 PHE 0.038 0.001 PHE A 408 TYR 0.019 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 289) hydrogen bonds : angle 4.79680 ( 843) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.94541 ( 2) covalent geometry : bond 0.00311 ( 4530) covalent geometry : angle 0.53094 ( 6178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.440 Fit side-chains REVERT: A 174 THR cc_start: 0.8538 (m) cc_final: 0.8140 (p) REVERT: A 373 LYS cc_start: 0.8490 (mmmm) cc_final: 0.7982 (mtmt) REVERT: A 403 PHE cc_start: 0.8099 (t80) cc_final: 0.7801 (t80) REVERT: A 418 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: A 500 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7211 (ttp-170) REVERT: A 507 GLN cc_start: 0.8316 (tt0) cc_final: 0.7866 (tt0) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.7424 time to fit residues: 52.9219 Evaluate side-chains 65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.138759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.115510 restraints weight = 4724.399| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.30 r_work: 0.3112 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4531 Z= 0.149 Angle : 0.556 7.502 6180 Z= 0.275 Chirality : 0.040 0.197 687 Planarity : 0.004 0.045 749 Dihedral : 4.625 43.345 590 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.83 % Allowed : 20.87 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.37), residues: 539 helix: 1.58 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.31 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.004 0.001 HIS A 599 PHE 0.037 0.001 PHE A 408 TYR 0.022 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 289) hydrogen bonds : angle 4.85850 ( 843) SS BOND : bond 0.00259 ( 1) SS BOND : angle 1.02525 ( 2) covalent geometry : bond 0.00366 ( 4530) covalent geometry : angle 0.55529 ( 6178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.434 Fit side-chains REVERT: A 373 LYS cc_start: 0.8494 (mmmm) cc_final: 0.7972 (mtmt) REVERT: A 403 PHE cc_start: 0.8132 (t80) cc_final: 0.7844 (t80) REVERT: A 418 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: A 500 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7257 (ttp-170) REVERT: A 507 GLN cc_start: 0.8367 (tt0) cc_final: 0.7915 (tt0) REVERT: A 556 TRP cc_start: 0.8155 (m100) cc_final: 0.6970 (m-10) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.6974 time to fit residues: 46.9280 Evaluate side-chains 64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.141782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.119294 restraints weight = 4766.697| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.22 r_work: 0.3152 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4531 Z= 0.131 Angle : 0.547 7.307 6180 Z= 0.272 Chirality : 0.039 0.187 687 Planarity : 0.004 0.046 749 Dihedral : 4.615 46.620 590 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.39 % Allowed : 21.30 % Favored : 76.30 % 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: 1.76 (0.37), residues: 539 helix: 1.58 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.33 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 521 HIS 0.003 0.001 HIS A 599 PHE 0.037 0.001 PHE A 408 TYR 0.019 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 289) hydrogen bonds : angle 4.83371 ( 843) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.90270 ( 2) covalent geometry : bond 0.00319 ( 4530) covalent geometry : angle 0.54711 ( 6178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.677 Fit side-chains REVERT: A 189 LYS cc_start: 0.7820 (mttp) cc_final: 0.7445 (pttm) REVERT: A 373 LYS cc_start: 0.8531 (mmmm) cc_final: 0.7996 (mtmt) REVERT: A 403 PHE cc_start: 0.8044 (t80) cc_final: 0.7778 (t80) REVERT: A 418 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: A 500 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7172 (ttp-170) REVERT: A 507 GLN cc_start: 0.8300 (tt0) cc_final: 0.7892 (tt0) REVERT: A 556 TRP cc_start: 0.8094 (m100) cc_final: 0.6910 (m-10) REVERT: A 574 ILE cc_start: 0.7349 (mp) cc_final: 0.7062 (tp) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 1.1312 time to fit residues: 82.1586 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.140307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.116969 restraints weight = 4727.439| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.32 r_work: 0.3128 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4531 Z= 0.142 Angle : 0.561 7.448 6180 Z= 0.279 Chirality : 0.041 0.230 687 Planarity : 0.004 0.044 749 Dihedral : 4.622 45.591 590 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.39 % Allowed : 21.30 % Favored : 76.30 % 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: 1.71 (0.37), residues: 539 helix: 1.52 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.36 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 PHE 0.037 0.001 PHE A 408 TYR 0.019 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 289) hydrogen bonds : angle 4.83566 ( 843) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.91195 ( 2) covalent geometry : bond 0.00347 ( 4530) covalent geometry : angle 0.56109 ( 6178) =============================================================================== Job complete usr+sys time: 3395.88 seconds wall clock time: 61 minutes 14.54 seconds (3674.54 seconds total)