Starting phenix.real_space_refine on Tue Mar 3 12:42:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r0m_53484/03_2026/9r0m_53484.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r0m_53484/03_2026/9r0m_53484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r0m_53484/03_2026/9r0m_53484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r0m_53484/03_2026/9r0m_53484.map" model { file = "/net/cci-nas-00/data/ceres_data/9r0m_53484/03_2026/9r0m_53484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r0m_53484/03_2026/9r0m_53484.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 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 35 5.16 5 C 2822 2.51 5 N 687 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4291 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4231 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 517} Chain breaks: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'P2E': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.01, per 1000 atoms: 0.24 Number of scatterers: 4291 At special positions: 0 Unit cell: (92.964, 83.448, 75.396, 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 35 16.00 O 747 8.00 N 687 7.00 C 2822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 494 " distance=2.04 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 594 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 390.2 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 69.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 Processing helix chain 'A' and resid 30 through 63 removed outlier: 3.655A pdb=" N PHE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 90 removed outlier: 4.591A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 115 Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.851A pdb=" N PHE A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 4.013A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.696A pdb=" N SER A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.529A pdb=" N ALA A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.682A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 324 through 357 removed outlier: 5.507A pdb=" N ASN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 370 Processing helix chain 'A' and resid 370 through 389 Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 514 through 531 removed outlier: 3.610A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.507A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 564 Processing helix chain 'A' and resid 566 through 578 removed outlier: 4.029A pdb=" N SER A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 460 removed outlier: 3.755A pdb=" N SER A 476 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.743A pdb=" N TYR A 596 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP A 583 " --> pdb=" O CYS A 594 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N CYS A 594 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR A 585 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY A 592 " --> pdb=" O TYR A 585 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.61 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: 817 1.33 - 1.45: 1105 1.45 - 1.58: 2432 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 4405 Sorted by residual: bond pdb=" N SER A 26 " pdb=" CA SER A 26 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" CB ASN A 604 " pdb=" CG ASN A 604 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.38e-01 bond pdb=" C ASN A 604 " pdb=" O ASN A 604 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.26e-02 6.30e+03 5.30e-01 bond pdb=" CG1 ILE A 367 " pdb=" CD1 ILE A 367 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.23e-01 bond pdb=" C TYR A 606 " pdb=" O TYR A 606 " ideal model delta sigma weight residual 1.236 1.244 -0.008 1.15e-02 7.56e+03 4.70e-01 ... (remaining 4400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 5656 1.00 - 2.00: 249 2.00 - 3.00: 53 3.00 - 4.00: 24 4.00 - 5.01: 8 Bond angle restraints: 5990 Sorted by residual: angle pdb=" C ARG A 603 " pdb=" N ASN A 604 " pdb=" CA ASN A 604 " ideal model delta sigma weight residual 120.31 117.26 3.05 1.52e+00 4.33e-01 4.04e+00 angle pdb=" CAR Y01 A 702 " pdb=" CBC Y01 A 702 " pdb=" CAV Y01 A 702 " ideal model delta sigma weight residual 110.42 115.22 -4.80 3.00e+00 1.11e-01 2.56e+00 angle pdb=" CA TYR A 606 " pdb=" CB TYR A 606 " pdb=" CG TYR A 606 " ideal model delta sigma weight residual 113.90 116.64 -2.74 1.80e+00 3.09e-01 2.32e+00 angle pdb=" C THR A 346 " pdb=" N PHE A 347 " pdb=" CA PHE A 347 " ideal model delta sigma weight residual 122.29 119.99 2.30 1.56e+00 4.11e-01 2.16e+00 angle pdb=" CA TYR A 51 " pdb=" CB TYR A 51 " pdb=" CG TYR A 51 " ideal model delta sigma weight residual 113.90 111.30 2.60 1.80e+00 3.09e-01 2.09e+00 ... (remaining 5985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 2383 17.49 - 34.98: 221 34.98 - 52.46: 55 52.46 - 69.95: 14 69.95 - 87.44: 3 Dihedral angle restraints: 2676 sinusoidal: 1087 harmonic: 1589 Sorted by residual: dihedral pdb=" CB CYS A 444 " pdb=" SG CYS A 444 " pdb=" SG CYS A 494 " pdb=" CB CYS A 494 " ideal model delta sinusoidal sigma weight residual -86.00 -18.94 -67.06 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CA CYS A 494 " pdb=" C CYS A 494 " pdb=" N VAL A 495 " pdb=" CA VAL A 495 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CB CYS A 450 " pdb=" SG CYS A 450 " pdb=" SG CYS A 470 " pdb=" CB CYS A 470 " ideal model delta sinusoidal sigma weight residual -86.00 -60.32 -25.68 1 1.00e+01 1.00e-02 9.48e+00 ... (remaining 2673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 419 0.028 - 0.056: 177 0.056 - 0.083: 56 0.083 - 0.111: 32 0.111 - 0.139: 6 Chirality restraints: 690 Sorted by residual: chirality pdb=" CB THR A 346 " pdb=" CA THR A 346 " pdb=" OG1 THR A 346 " pdb=" CG2 THR A 346 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE A 488 " pdb=" N ILE A 488 " pdb=" C ILE A 488 " pdb=" CB ILE A 488 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 687 not shown) Planarity restraints: 741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 516 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 517 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 310 " -0.008 2.00e-02 2.50e+03 9.47e-03 1.57e+00 pdb=" CG PHE A 310 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 310 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 310 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 310 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 310 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 412 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 413 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " 0.017 5.00e-02 4.00e+02 ... (remaining 738 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 2148 2.96 - 3.45: 4553 3.45 - 3.93: 6794 3.93 - 4.42: 7982 4.42 - 4.90: 13118 Nonbonded interactions: 34595 Sorted by model distance: nonbonded pdb=" OH TYR A 356 " pdb=" OG SER A 518 " model vdw 2.481 3.040 nonbonded pdb=" O ARG A 445 " pdb=" O CYS A 448 " model vdw 2.506 3.040 nonbonded pdb=" O4 P2E A 701 " pdb=" O5 P2E A 701 " model vdw 2.554 3.040 nonbonded pdb=" N GLU A 123 " pdb=" OE1 GLU A 123 " model vdw 2.568 3.120 nonbonded pdb=" O ILE A 85 " pdb=" OG SER A 89 " model vdw 2.575 3.040 ... (remaining 34590 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: 6.960 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.170 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4411 Z= 0.156 Angle : 0.557 5.006 6002 Z= 0.281 Chirality : 0.038 0.139 690 Planarity : 0.004 0.032 741 Dihedral : 14.509 87.439 1638 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.71 % Allowed : 11.78 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.37), residues: 544 helix: 2.23 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.57 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 627 TYR 0.014 0.001 TYR A 606 PHE 0.021 0.001 PHE A 310 TRP 0.003 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4405) covalent geometry : angle 0.55370 ( 5990) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.39040 ( 12) hydrogen bonds : bond 0.12534 ( 274) hydrogen bonds : angle 5.53023 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.172 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.0948 time to fit residues: 8.2308 Evaluate side-chains 51 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 509 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 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 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.102335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080110 restraints weight = 8575.545| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.87 r_work: 0.3065 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4411 Z= 0.134 Angle : 0.598 7.069 6002 Z= 0.284 Chirality : 0.041 0.166 690 Planarity : 0.004 0.035 741 Dihedral : 8.461 89.445 701 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.57 % Allowed : 14.35 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.37), residues: 544 helix: 2.62 (0.28), residues: 350 sheet: None (None), residues: 0 loop : 0.93 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.012 0.001 TYR A 606 PHE 0.013 0.001 PHE A 198 TRP 0.008 0.001 TRP A 170 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4405) covalent geometry : angle 0.59814 ( 5990) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.68344 ( 12) hydrogen bonds : bond 0.04266 ( 274) hydrogen bonds : angle 4.16222 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 454 PHE cc_start: 0.7716 (m-80) cc_final: 0.7411 (m-80) outliers start: 12 outliers final: 5 residues processed: 61 average time/residue: 0.0517 time to fit residues: 4.2060 Evaluate side-chains 49 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** 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 = 0.3540 r_free = 0.3540 target = 0.100211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.078203 restraints weight = 8710.840| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.83 r_work: 0.3032 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4411 Z= 0.170 Angle : 0.597 7.829 6002 Z= 0.283 Chirality : 0.043 0.166 690 Planarity : 0.004 0.039 741 Dihedral : 8.332 88.484 696 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.85 % Allowed : 13.28 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.37), residues: 544 helix: 2.63 (0.28), residues: 355 sheet: None (None), residues: 0 loop : 0.94 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.025 0.002 TYR A 572 PHE 0.014 0.001 PHE A 198 TRP 0.005 0.001 TRP A 257 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 4405) covalent geometry : angle 0.59665 ( 5990) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.73558 ( 12) hydrogen bonds : bond 0.04335 ( 274) hydrogen bonds : angle 3.98896 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8244 (pt0) cc_final: 0.8000 (pm20) REVERT: A 386 MET cc_start: 0.8956 (tpp) cc_final: 0.8671 (tpp) REVERT: A 454 PHE cc_start: 0.7678 (m-80) cc_final: 0.7180 (m-80) REVERT: A 490 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 516 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8366 (mm) outliers start: 18 outliers final: 9 residues processed: 61 average time/residue: 0.0566 time to fit residues: 4.7080 Evaluate side-chains 54 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.102665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080599 restraints weight = 8536.551| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.77 r_work: 0.3094 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4411 Z= 0.128 Angle : 0.554 6.638 6002 Z= 0.264 Chirality : 0.042 0.150 690 Planarity : 0.004 0.042 741 Dihedral : 8.417 84.609 696 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.36 % Allowed : 15.42 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.37), residues: 544 helix: 2.77 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 0.83 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.017 0.001 TYR A 572 PHE 0.010 0.001 PHE A 198 TRP 0.003 0.001 TRP A 257 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4405) covalent geometry : angle 0.55379 ( 5990) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.78556 ( 12) hydrogen bonds : bond 0.03838 ( 274) hydrogen bonds : angle 3.81646 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 386 MET cc_start: 0.8911 (tpp) cc_final: 0.8255 (tpp) REVERT: A 454 PHE cc_start: 0.7650 (m-80) cc_final: 0.7179 (m-80) REVERT: A 490 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8575 (mp) outliers start: 11 outliers final: 10 residues processed: 54 average time/residue: 0.0519 time to fit residues: 3.9466 Evaluate side-chains 53 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS A 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.102285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080294 restraints weight = 8628.378| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.77 r_work: 0.3089 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4411 Z= 0.133 Angle : 0.549 6.236 6002 Z= 0.261 Chirality : 0.041 0.142 690 Planarity : 0.004 0.042 741 Dihedral : 8.437 84.365 696 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.00 % Allowed : 15.63 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.37), residues: 544 helix: 2.84 (0.27), residues: 354 sheet: None (None), residues: 0 loop : 0.90 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 627 TYR 0.011 0.001 TYR A 572 PHE 0.010 0.001 PHE A 198 TRP 0.004 0.001 TRP A 257 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4405) covalent geometry : angle 0.54873 ( 5990) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.78808 ( 12) hydrogen bonds : bond 0.03828 ( 274) hydrogen bonds : angle 3.75525 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.169 Fit side-chains REVERT: A 454 PHE cc_start: 0.7624 (m-80) cc_final: 0.7145 (m-80) REVERT: A 490 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 516 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8415 (mm) outliers start: 14 outliers final: 9 residues processed: 56 average time/residue: 0.0585 time to fit residues: 4.4995 Evaluate side-chains 53 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080279 restraints weight = 8804.596| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.81 r_work: 0.3094 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4411 Z= 0.135 Angle : 0.563 6.674 6002 Z= 0.270 Chirality : 0.041 0.139 690 Planarity : 0.004 0.041 741 Dihedral : 8.425 84.150 695 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.57 % Allowed : 16.06 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.37), residues: 544 helix: 2.86 (0.28), residues: 354 sheet: None (None), residues: 0 loop : 0.93 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 62 TYR 0.013 0.001 TYR A 613 PHE 0.011 0.001 PHE A 198 TRP 0.004 0.001 TRP A 257 HIS 0.001 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4405) covalent geometry : angle 0.56214 ( 5990) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.72719 ( 12) hydrogen bonds : bond 0.03863 ( 274) hydrogen bonds : angle 3.73393 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.136 Fit side-chains REVERT: A 386 MET cc_start: 0.8877 (tpp) cc_final: 0.8396 (tpp) REVERT: A 454 PHE cc_start: 0.7586 (m-80) cc_final: 0.7123 (m-80) REVERT: A 490 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8580 (mp) REVERT: A 516 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (mm) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.0482 time to fit residues: 3.5416 Evaluate side-chains 52 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.103276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081413 restraints weight = 8795.102| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.84 r_work: 0.3110 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4411 Z= 0.116 Angle : 0.539 6.696 6002 Z= 0.257 Chirality : 0.041 0.134 690 Planarity : 0.004 0.041 741 Dihedral : 8.371 83.058 695 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.21 % Allowed : 15.20 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.37), residues: 544 helix: 2.92 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 0.95 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 446 TYR 0.011 0.001 TYR A 613 PHE 0.008 0.001 PHE A 198 TRP 0.003 0.001 TRP A 626 HIS 0.001 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4405) covalent geometry : angle 0.53848 ( 5990) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.65120 ( 12) hydrogen bonds : bond 0.03600 ( 274) hydrogen bonds : angle 3.65031 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.138 Fit side-chains REVERT: A 386 MET cc_start: 0.8888 (tpp) cc_final: 0.8393 (tpp) REVERT: A 454 PHE cc_start: 0.7598 (m-80) cc_final: 0.7127 (m-80) REVERT: A 490 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8591 (mp) REVERT: A 516 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8430 (mm) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.0401 time to fit residues: 3.2834 Evaluate side-chains 54 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.103358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081595 restraints weight = 8677.524| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.77 r_work: 0.3109 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4411 Z= 0.119 Angle : 0.542 7.063 6002 Z= 0.258 Chirality : 0.040 0.135 690 Planarity : 0.004 0.041 741 Dihedral : 8.327 82.514 695 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.00 % Allowed : 15.63 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.37), residues: 544 helix: 2.93 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 0.96 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 320 TYR 0.012 0.001 TYR A 613 PHE 0.009 0.001 PHE A 198 TRP 0.003 0.001 TRP A 170 HIS 0.001 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4405) covalent geometry : angle 0.54144 ( 5990) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.80519 ( 12) hydrogen bonds : bond 0.03609 ( 274) hydrogen bonds : angle 3.65511 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.163 Fit side-chains REVERT: A 60 GLU cc_start: 0.8524 (pp20) cc_final: 0.8197 (pp20) REVERT: A 386 MET cc_start: 0.8920 (tpp) cc_final: 0.8582 (tpp) REVERT: A 454 PHE cc_start: 0.7587 (m-80) cc_final: 0.7104 (m-80) REVERT: A 490 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 516 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8408 (mm) outliers start: 14 outliers final: 10 residues processed: 56 average time/residue: 0.0451 time to fit residues: 3.6373 Evaluate side-chains 55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.103556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081793 restraints weight = 8723.079| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.88 r_work: 0.3118 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4411 Z= 0.115 Angle : 0.538 7.205 6002 Z= 0.256 Chirality : 0.040 0.137 690 Planarity : 0.004 0.040 741 Dihedral : 8.278 81.673 695 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.57 % Allowed : 16.49 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.37), residues: 544 helix: 2.96 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 0.93 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 320 TYR 0.013 0.001 TYR A 613 PHE 0.008 0.001 PHE A 198 TRP 0.003 0.001 TRP A 170 HIS 0.001 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4405) covalent geometry : angle 0.53734 ( 5990) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.75111 ( 12) hydrogen bonds : bond 0.03546 ( 274) hydrogen bonds : angle 3.62131 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.129 Fit side-chains REVERT: A 60 GLU cc_start: 0.8551 (pp20) cc_final: 0.8216 (pp20) REVERT: A 386 MET cc_start: 0.8957 (tpp) cc_final: 0.8552 (tpp) REVERT: A 454 PHE cc_start: 0.7557 (m-80) cc_final: 0.7100 (m-80) REVERT: A 490 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 516 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8423 (mm) outliers start: 12 outliers final: 10 residues processed: 54 average time/residue: 0.0432 time to fit residues: 3.3353 Evaluate side-chains 55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 48 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.3312 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.104695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083066 restraints weight = 8666.429| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.78 r_work: 0.3142 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4411 Z= 0.102 Angle : 0.531 7.209 6002 Z= 0.253 Chirality : 0.040 0.137 690 Planarity : 0.004 0.040 741 Dihedral : 8.218 80.463 695 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.14 % Allowed : 16.92 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.37), residues: 544 helix: 3.01 (0.28), residues: 353 sheet: None (None), residues: 0 loop : 0.90 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.013 0.001 TYR A 613 PHE 0.007 0.001 PHE A 198 TRP 0.004 0.001 TRP A 626 HIS 0.001 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4405) covalent geometry : angle 0.53074 ( 5990) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.67025 ( 12) hydrogen bonds : bond 0.03368 ( 274) hydrogen bonds : angle 3.55362 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.161 Fit side-chains REVERT: A 60 GLU cc_start: 0.8560 (pp20) cc_final: 0.8219 (pp20) REVERT: A 386 MET cc_start: 0.8951 (tpp) cc_final: 0.8531 (tpp) REVERT: A 454 PHE cc_start: 0.7517 (m-80) cc_final: 0.7060 (m-80) REVERT: A 516 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8419 (mm) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.0488 time to fit residues: 3.6367 Evaluate side-chains 51 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 540 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.103886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082076 restraints weight = 8697.874| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.87 r_work: 0.3128 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4411 Z= 0.116 Angle : 0.545 7.351 6002 Z= 0.257 Chirality : 0.041 0.155 690 Planarity : 0.004 0.040 741 Dihedral : 8.179 79.818 695 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.14 % Allowed : 17.13 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.37), residues: 544 helix: 3.01 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 0.94 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 320 TYR 0.014 0.001 TYR A 613 PHE 0.009 0.001 PHE A 198 TRP 0.004 0.001 TRP A 257 HIS 0.001 0.000 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4405) covalent geometry : angle 0.54475 ( 5990) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.70503 ( 12) hydrogen bonds : bond 0.03470 ( 274) hydrogen bonds : angle 3.56221 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1185.43 seconds wall clock time: 21 minutes 0.76 seconds (1260.76 seconds total)