Starting phenix.real_space_refine on Wed Jun 4 19:51:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s61_19754/06_2025/8s61_19754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s61_19754/06_2025/8s61_19754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s61_19754/06_2025/8s61_19754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s61_19754/06_2025/8s61_19754.map" model { file = "/net/cci-nas-00/data/ceres_data/8s61_19754/06_2025/8s61_19754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s61_19754/06_2025/8s61_19754.cif" } resolution = 3.53 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2647 2.51 5 N 624 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3990 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 935 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3037 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.72, per 1000 atoms: 0.93 Number of scatterers: 3990 At special positions: 0 Unit cell: (92.13, 83.83, 75.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 698 8.00 N 624 7.00 C 2647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 1.03 Conformation dependent library (CDL) restraints added in 513.0 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 60.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 removed outlier: 3.851A pdb=" N THR A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 56 through 66 removed outlier: 4.333A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.779A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 removed outlier: 4.386A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 removed outlier: 3.566A pdb=" N GLN A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.753A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 removed outlier: 4.206A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.528A pdb=" N VAL A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.179A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.571A pdb=" N TRP A 285 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 315 through 335 removed outlier: 3.529A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.844A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.621A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 426 removed outlier: 4.381A pdb=" N ILE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 removed outlier: 4.182A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.549A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.385A pdb=" N ARG B 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 600 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: 1.28 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 680 1.33 - 1.45: 1184 1.45 - 1.57: 2204 1.57 - 1.69: 1 1.69 - 1.81: 34 Bond restraints: 4103 Sorted by residual: bond pdb=" C5 VIB A 601 " pdb=" S1 VIB A 601 " ideal model delta sigma weight residual 1.721 1.511 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C4 VIB A 601 " pdb=" N3 VIB A 601 " ideal model delta sigma weight residual 1.385 1.570 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" C2A VIB A 601 " pdb=" N3A VIB A 601 " ideal model delta sigma weight residual 1.323 1.483 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C2A VIB A 601 " pdb=" N1A VIB A 601 " ideal model delta sigma weight residual 1.331 1.483 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C2 VIB A 601 " pdb=" S1 VIB A 601 " ideal model delta sigma weight residual 1.670 1.537 0.133 2.00e-02 2.50e+03 4.42e+01 ... (remaining 4098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 5564 3.30 - 6.60: 29 6.60 - 9.90: 1 9.90 - 13.20: 0 13.20 - 16.51: 1 Bond angle restraints: 5595 Sorted by residual: angle pdb=" C2 VIB A 601 " pdb=" S1 VIB A 601 " pdb=" C5 VIB A 601 " ideal model delta sigma weight residual 91.25 107.76 -16.51 3.00e+00 1.11e-01 3.03e+01 angle pdb=" N ASN A 173 " pdb=" CA ASN A 173 " pdb=" C ASN A 173 " ideal model delta sigma weight residual 112.23 105.56 6.67 1.26e+00 6.30e-01 2.80e+01 angle pdb=" N SER B 17 " pdb=" CA SER B 17 " pdb=" C SER B 17 " ideal model delta sigma weight residual 110.41 115.36 -4.95 1.23e+00 6.61e-01 1.62e+01 angle pdb=" N ILE A 449 " pdb=" CA ILE A 449 " pdb=" C ILE A 449 " ideal model delta sigma weight residual 112.80 108.41 4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N LEU A 160 " pdb=" CA LEU A 160 " pdb=" C LEU A 160 " ideal model delta sigma weight residual 113.88 109.51 4.37 1.23e+00 6.61e-01 1.26e+01 ... (remaining 5590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2033 17.85 - 35.71: 224 35.71 - 53.56: 61 53.56 - 71.41: 11 71.41 - 89.26: 4 Dihedral angle restraints: 2333 sinusoidal: 861 harmonic: 1472 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 142.97 -49.97 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR A 171 " pdb=" C TYR A 171 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 417 0.032 - 0.064: 145 0.064 - 0.095: 47 0.095 - 0.127: 17 0.127 - 0.159: 4 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA ASN B 32 " pdb=" N ASN B 32 " pdb=" C ASN B 32 " pdb=" CB ASN B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 627 not shown) Planarity restraints: 682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 87 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO B 88 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 172 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C LEU A 172 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 172 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 173 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 73 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.33e+00 pdb=" C ASP B 73 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP B 73 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 74 " -0.010 2.00e-02 2.50e+03 ... (remaining 679 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 23 2.57 - 3.16: 3363 3.16 - 3.74: 5880 3.74 - 4.32: 8341 4.32 - 4.90: 14385 Nonbonded interactions: 31992 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" O1 VIB A 601 " model vdw 1.994 3.040 nonbonded pdb=" OE1 GLN A 159 " pdb=" OG SER A 163 " model vdw 2.200 3.040 nonbonded pdb=" O TYR A 76 " pdb=" NE2 HIS A 200 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 277 " pdb=" O GLN A 393 " model vdw 2.328 3.120 nonbonded pdb=" OE1 GLU A 110 " pdb=" N4A VIB A 601 " model vdw 2.364 3.120 ... (remaining 31987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.250 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.930 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.008 0.210 4104 Z= 0.454 Angle : 0.625 16.505 5597 Z= 0.349 Chirality : 0.039 0.159 630 Planarity : 0.004 0.066 682 Dihedral : 16.574 89.265 1394 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 19.48 % Favored : 80.52 % 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: -1.96 (0.38), residues: 496 helix: -1.07 (0.31), residues: 280 sheet: -2.36 (0.77), residues: 52 loop : -0.96 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS A 135 PHE 0.014 0.001 PHE A 198 TYR 0.005 0.001 TYR B 47 ARG 0.002 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.26232 ( 210) hydrogen bonds : angle 9.20618 ( 600) SS BOND : bond 0.00348 ( 1) SS BOND : angle 0.86095 ( 2) covalent geometry : bond 0.00846 ( 4103) covalent geometry : angle 0.62506 ( 5595) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.385 Fit side-chains REVERT: A 198 PHE cc_start: 0.7743 (m-80) cc_final: 0.5705 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1801 time to fit residues: 11.0737 Evaluate side-chains 47 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.138178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.127961 restraints weight = 4609.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.128524 restraints weight = 3970.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.129398 restraints weight = 3559.723| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4104 Z= 0.235 Angle : 0.646 6.117 5597 Z= 0.340 Chirality : 0.043 0.168 630 Planarity : 0.005 0.058 682 Dihedral : 5.867 64.069 556 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.61 % Allowed : 19.24 % Favored : 78.15 % 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: -1.06 (0.39), residues: 496 helix: -0.10 (0.32), residues: 282 sheet: -1.48 (0.97), residues: 37 loop : -1.33 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 284 HIS 0.003 0.002 HIS A 364 PHE 0.016 0.002 PHE A 439 TYR 0.013 0.002 TYR A 280 ARG 0.002 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.05324 ( 210) hydrogen bonds : angle 4.92738 ( 600) SS BOND : bond 0.00909 ( 1) SS BOND : angle 1.85230 ( 2) covalent geometry : bond 0.00584 ( 4103) covalent geometry : angle 0.64544 ( 5595) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.469 Fit side-chains REVERT: A 198 PHE cc_start: 0.7847 (m-80) cc_final: 0.6480 (t80) outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 0.1665 time to fit residues: 10.7046 Evaluate side-chains 44 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain A residue 167 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 34 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.145720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.135442 restraints weight = 4505.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136296 restraints weight = 3685.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.136825 restraints weight = 3203.562| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4104 Z= 0.147 Angle : 0.538 5.421 5597 Z= 0.286 Chirality : 0.040 0.168 630 Planarity : 0.004 0.060 682 Dihedral : 5.720 68.780 556 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.80 % Allowed : 19.00 % Favored : 77.20 % 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: -0.60 (0.39), residues: 496 helix: 0.31 (0.33), residues: 282 sheet: -1.07 (0.94), residues: 37 loop : -1.28 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.010 0.001 TYR A 383 ARG 0.001 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 210) hydrogen bonds : angle 4.23005 ( 600) SS BOND : bond 0.00581 ( 1) SS BOND : angle 1.19522 ( 2) covalent geometry : bond 0.00353 ( 4103) covalent geometry : angle 0.53803 ( 5595) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.447 Fit side-chains REVERT: A 18 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7833 (mm) REVERT: A 198 PHE cc_start: 0.7841 (m-80) cc_final: 0.6433 (t80) outliers start: 16 outliers final: 10 residues processed: 55 average time/residue: 0.1531 time to fit residues: 11.2551 Evaluate side-chains 52 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.142528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.132171 restraints weight = 4557.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133102 restraints weight = 3738.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133968 restraints weight = 3244.210| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4104 Z= 0.191 Angle : 0.582 7.866 5597 Z= 0.303 Chirality : 0.042 0.167 630 Planarity : 0.004 0.059 682 Dihedral : 5.859 68.987 556 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.75 % Allowed : 19.48 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.39), residues: 496 helix: 0.28 (0.33), residues: 282 sheet: -0.91 (0.94), residues: 35 loop : -1.34 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE A 439 TYR 0.009 0.001 TYR B 47 ARG 0.002 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 210) hydrogen bonds : angle 4.20304 ( 600) SS BOND : bond 0.00744 ( 1) SS BOND : angle 1.68604 ( 2) covalent geometry : bond 0.00473 ( 4103) covalent geometry : angle 0.58171 ( 5595) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.403 Fit side-chains REVERT: A 18 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7943 (mm) REVERT: A 198 PHE cc_start: 0.7951 (m-80) cc_final: 0.6622 (t80) REVERT: A 421 MET cc_start: 0.8484 (ttp) cc_final: 0.8135 (ptt) outliers start: 20 outliers final: 14 residues processed: 60 average time/residue: 0.1419 time to fit residues: 11.2483 Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 405 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.0060 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.139222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128978 restraints weight = 4682.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129944 restraints weight = 3898.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130390 restraints weight = 3401.648| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4104 Z= 0.139 Angle : 0.528 5.973 5597 Z= 0.275 Chirality : 0.040 0.165 630 Planarity : 0.004 0.057 682 Dihedral : 5.697 70.834 556 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.04 % Allowed : 19.95 % Favored : 76.01 % 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: -0.44 (0.39), residues: 496 helix: 0.46 (0.33), residues: 282 sheet: -0.90 (0.90), residues: 37 loop : -1.26 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.010 0.001 PHE A 439 TYR 0.011 0.001 TYR A 14 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 210) hydrogen bonds : angle 3.90968 ( 600) SS BOND : bond 0.00468 ( 1) SS BOND : angle 1.17111 ( 2) covalent geometry : bond 0.00334 ( 4103) covalent geometry : angle 0.52786 ( 5595) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.402 Fit side-chains REVERT: A 18 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 198 PHE cc_start: 0.7946 (m-80) cc_final: 0.6565 (t80) outliers start: 17 outliers final: 14 residues processed: 57 average time/residue: 0.1467 time to fit residues: 10.7691 Evaluate side-chains 57 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.137298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.127186 restraints weight = 4569.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.127982 restraints weight = 3882.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.128814 restraints weight = 3429.216| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4104 Z= 0.162 Angle : 0.546 5.489 5597 Z= 0.284 Chirality : 0.041 0.164 630 Planarity : 0.004 0.056 682 Dihedral : 5.740 70.048 556 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.23 % Allowed : 19.71 % Favored : 75.06 % 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: -0.41 (0.39), residues: 496 helix: 0.47 (0.33), residues: 282 sheet: -0.68 (0.93), residues: 35 loop : -1.27 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.001 PHE A 439 TYR 0.017 0.001 TYR A 336 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 210) hydrogen bonds : angle 3.92904 ( 600) SS BOND : bond 0.00609 ( 1) SS BOND : angle 1.50068 ( 2) covalent geometry : bond 0.00398 ( 4103) covalent geometry : angle 0.54490 ( 5595) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.420 Fit side-chains REVERT: A 18 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7912 (mm) REVERT: A 198 PHE cc_start: 0.8056 (m-80) cc_final: 0.6663 (t80) outliers start: 22 outliers final: 19 residues processed: 60 average time/residue: 0.1415 time to fit residues: 11.1511 Evaluate side-chains 64 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 458 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.137594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127568 restraints weight = 4641.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.128286 restraints weight = 3897.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.129083 restraints weight = 3457.425| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4104 Z= 0.157 Angle : 0.540 5.472 5597 Z= 0.282 Chirality : 0.041 0.164 630 Planarity : 0.004 0.056 682 Dihedral : 5.740 70.316 556 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.75 % Allowed : 20.67 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.39), residues: 496 helix: 0.52 (0.33), residues: 282 sheet: -0.86 (0.83), residues: 43 loop : -1.33 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.018 0.001 TYR A 336 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 210) hydrogen bonds : angle 3.86915 ( 600) SS BOND : bond 0.00567 ( 1) SS BOND : angle 1.44405 ( 2) covalent geometry : bond 0.00385 ( 4103) covalent geometry : angle 0.53891 ( 5595) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.422 Fit side-chains REVERT: A 198 PHE cc_start: 0.8066 (m-80) cc_final: 0.6712 (t80) REVERT: A 421 MET cc_start: 0.8412 (ttp) cc_final: 0.8202 (ptt) outliers start: 20 outliers final: 16 residues processed: 61 average time/residue: 0.1418 time to fit residues: 11.2624 Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 19 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 = 0.3337 r_free = 0.3337 target = 0.130236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.120106 restraints weight = 4702.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.120613 restraints weight = 4069.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.120614 restraints weight = 3690.296| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4104 Z= 0.207 Angle : 0.617 10.690 5597 Z= 0.312 Chirality : 0.043 0.166 630 Planarity : 0.004 0.057 682 Dihedral : 5.960 69.783 556 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.80 % Allowed : 21.85 % Favored : 74.35 % 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: -0.51 (0.39), residues: 496 helix: 0.40 (0.32), residues: 282 sheet: -0.99 (0.84), residues: 42 loop : -1.29 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.015 0.001 PHE A 439 TYR 0.020 0.001 TYR A 336 ARG 0.002 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 210) hydrogen bonds : angle 4.06757 ( 600) SS BOND : bond 0.00761 ( 1) SS BOND : angle 1.92914 ( 2) covalent geometry : bond 0.00514 ( 4103) covalent geometry : angle 0.61580 ( 5595) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.449 Fit side-chains REVERT: A 198 PHE cc_start: 0.8106 (m-80) cc_final: 0.6682 (t80) outliers start: 16 outliers final: 15 residues processed: 56 average time/residue: 0.1405 time to fit residues: 10.4139 Evaluate side-chains 58 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 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 = 0.3351 r_free = 0.3351 target = 0.131448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.121143 restraints weight = 4723.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.121729 restraints weight = 3972.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.122505 restraints weight = 3589.381| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4104 Z= 0.183 Angle : 0.590 9.794 5597 Z= 0.299 Chirality : 0.042 0.167 630 Planarity : 0.004 0.057 682 Dihedral : 5.904 70.205 556 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.04 % Allowed : 21.85 % Favored : 74.11 % 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: -0.47 (0.39), residues: 496 helix: 0.45 (0.32), residues: 282 sheet: -0.92 (0.84), residues: 42 loop : -1.30 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.013 0.001 PHE A 439 TYR 0.011 0.001 TYR A 336 ARG 0.002 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 210) hydrogen bonds : angle 3.97659 ( 600) SS BOND : bond 0.00650 ( 1) SS BOND : angle 1.75864 ( 2) covalent geometry : bond 0.00450 ( 4103) covalent geometry : angle 0.58956 ( 5595) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.458 Fit side-chains REVERT: A 198 PHE cc_start: 0.8138 (m-80) cc_final: 0.6739 (t80) REVERT: A 385 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8895 (tt) outliers start: 17 outliers final: 15 residues processed: 60 average time/residue: 0.1501 time to fit residues: 11.7015 Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 385 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.0060 chunk 28 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.140621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.130125 restraints weight = 4628.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130791 restraints weight = 3892.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131577 restraints weight = 3479.646| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4104 Z= 0.162 Angle : 0.569 9.515 5597 Z= 0.289 Chirality : 0.041 0.165 630 Planarity : 0.004 0.056 682 Dihedral : 5.833 69.939 556 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.51 % Allowed : 21.62 % Favored : 73.87 % 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: -0.36 (0.39), residues: 496 helix: 0.51 (0.32), residues: 282 sheet: -0.56 (0.93), residues: 35 loop : -1.29 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.011 0.001 TYR A 336 ARG 0.001 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 210) hydrogen bonds : angle 3.94970 ( 600) SS BOND : bond 0.00565 ( 1) SS BOND : angle 1.51819 ( 2) covalent geometry : bond 0.00399 ( 4103) covalent geometry : angle 0.56834 ( 5595) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.456 Fit side-chains REVERT: A 198 PHE cc_start: 0.8146 (m-80) cc_final: 0.6822 (t80) REVERT: A 385 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8824 (tt) outliers start: 19 outliers final: 15 residues processed: 60 average time/residue: 0.1746 time to fit residues: 13.5255 Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 385 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.0770 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.131959 restraints weight = 4562.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.132929 restraints weight = 3843.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133737 restraints weight = 3356.268| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4104 Z= 0.141 Angle : 0.548 9.178 5597 Z= 0.279 Chirality : 0.041 0.163 630 Planarity : 0.004 0.055 682 Dihedral : 5.738 69.706 556 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.75 % Allowed : 21.38 % Favored : 73.87 % 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: -0.33 (0.39), residues: 496 helix: 0.58 (0.32), residues: 283 sheet: -0.68 (0.84), residues: 43 loop : -1.35 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.019 0.001 PHE A 71 TYR 0.011 0.001 TYR A 336 ARG 0.001 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 210) hydrogen bonds : angle 3.86404 ( 600) SS BOND : bond 0.00477 ( 1) SS BOND : angle 1.34375 ( 2) covalent geometry : bond 0.00340 ( 4103) covalent geometry : angle 0.54759 ( 5595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.21 seconds wall clock time: 30 minutes 33.21 seconds (1833.21 seconds total)