Starting phenix.real_space_refine on Tue Feb 3 16:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxk_61866/02_2026/9jxk_61866.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxk_61866/02_2026/9jxk_61866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxk_61866/02_2026/9jxk_61866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxk_61866/02_2026/9jxk_61866.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxk_61866/02_2026/9jxk_61866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxk_61866/02_2026/9jxk_61866.cif" } resolution = 3.38 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= 0.005 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 3298 2.51 5 N 823 2.21 5 O 867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5011 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 5001 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 20, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.85, per 1000 atoms: 0.17 Number of scatterers: 5011 At special positions: 0 Unit cell: (100.225, 70.685, 103.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 2 15.00 O 867 8.00 N 823 7.00 C 3298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.02 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: 0.37 Conformation dependent library (CDL) restraints added in 283.9 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 12 through 19 removed outlier: 3.704A pdb=" N ARG B 16 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 43 through 99 removed outlier: 3.801A pdb=" N LYS B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 168 removed outlier: 3.614A pdb=" N LEU B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.886A pdb=" N GLN B 227 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.041A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.579A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.644A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.518A pdb=" N PHE B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.195A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 480 through 503 removed outlier: 3.675A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.640A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.824A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.907A pdb=" N GLN B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 596 through 618 removed outlier: 3.714A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1056 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: 0.48 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 768 1.29 - 1.42: 1496 1.42 - 1.55: 2857 1.55 - 1.68: 3 1.68 - 1.81: 30 Bond restraints: 5154 Sorted by residual: bond pdb=" CA GLY B 438 " pdb=" C GLY B 438 " ideal model delta sigma weight residual 1.516 1.452 0.064 1.04e-02 9.25e+03 3.74e+01 bond pdb=" C PRO B 475 " pdb=" O PRO B 475 " ideal model delta sigma weight residual 1.238 1.160 0.078 1.33e-02 5.65e+03 3.47e+01 bond pdb=" N PRO B 475 " pdb=" CA PRO B 475 " ideal model delta sigma weight residual 1.471 1.418 0.052 1.32e-02 5.74e+03 1.58e+01 bond pdb=" C GLY B 438 " pdb=" N ILE B 439 " ideal model delta sigma weight residual 1.335 1.286 0.049 1.26e-02 6.30e+03 1.50e+01 bond pdb=" N VAL B 595 " pdb=" CA VAL B 595 " ideal model delta sigma weight residual 1.459 1.493 -0.034 9.10e-03 1.21e+04 1.41e+01 ... (remaining 5149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 6801 2.73 - 5.46: 146 5.46 - 8.20: 35 8.20 - 10.93: 5 10.93 - 13.66: 2 Bond angle restraints: 6989 Sorted by residual: angle pdb=" C GLU B 435 " pdb=" N GLU B 436 " pdb=" CA GLU B 436 " ideal model delta sigma weight residual 123.14 109.48 13.66 1.48e+00 4.57e-01 8.52e+01 angle pdb=" N ILE B 577 " pdb=" CA ILE B 577 " pdb=" C ILE B 577 " ideal model delta sigma weight residual 110.62 102.83 7.79 1.02e+00 9.61e-01 5.83e+01 angle pdb=" C ASN B 618 " pdb=" CA ASN B 618 " pdb=" CB ASN B 618 " ideal model delta sigma weight residual 111.77 100.16 11.61 1.52e+00 4.33e-01 5.83e+01 angle pdb=" C CYS B 440 " pdb=" N HIS B 441 " pdb=" CA HIS B 441 " ideal model delta sigma weight residual 123.37 112.79 10.58 1.64e+00 3.72e-01 4.16e+01 angle pdb=" C HIS B 476 " pdb=" N LEU B 477 " pdb=" CA LEU B 477 " ideal model delta sigma weight residual 120.54 111.89 8.65 1.35e+00 5.49e-01 4.11e+01 ... (remaining 6984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2599 17.98 - 35.96: 315 35.96 - 53.94: 71 53.94 - 71.93: 10 71.93 - 89.91: 4 Dihedral angle restraints: 2999 sinusoidal: 1214 harmonic: 1785 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual -86.00 -167.98 81.98 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" C HIS B 476 " pdb=" N HIS B 476 " pdb=" CA HIS B 476 " pdb=" CB HIS B 476 " ideal model delta harmonic sigma weight residual -122.60 -134.26 11.66 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C THR B 574 " pdb=" N THR B 574 " pdb=" CA THR B 574 " pdb=" CB THR B 574 " ideal model delta harmonic sigma weight residual -122.00 -110.43 -11.57 0 2.50e+00 1.60e-01 2.14e+01 ... (remaining 2996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 675 0.075 - 0.150: 65 0.150 - 0.225: 15 0.225 - 0.300: 2 0.300 - 0.375: 1 Chirality restraints: 758 Sorted by residual: chirality pdb=" CA HIS B 476 " pdb=" N HIS B 476 " pdb=" C HIS B 476 " pdb=" CB HIS B 476 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA THR B 574 " pdb=" N THR B 574 " pdb=" C THR B 574 " pdb=" CB THR B 574 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA HIS B 587 " pdb=" N HIS B 587 " pdb=" C HIS B 587 " pdb=" CB HIS B 587 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 755 not shown) Planarity restraints: 869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 470 " -0.038 2.00e-02 2.50e+03 7.61e-02 5.79e+01 pdb=" C THR B 470 " 0.132 2.00e-02 2.50e+03 pdb=" O THR B 470 " -0.050 2.00e-02 2.50e+03 pdb=" N LYS B 471 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 434 " 0.027 2.00e-02 2.50e+03 5.69e-02 3.23e+01 pdb=" C SER B 434 " -0.098 2.00e-02 2.50e+03 pdb=" O SER B 434 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU B 435 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 438 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLY B 438 " 0.064 2.00e-02 2.50e+03 pdb=" O GLY B 438 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B 439 " -0.022 2.00e-02 2.50e+03 ... (remaining 866 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 77 2.58 - 3.16: 4219 3.16 - 3.74: 8177 3.74 - 4.32: 10370 4.32 - 4.90: 17584 Nonbonded interactions: 40427 Sorted by model distance: nonbonded pdb=" OD2 ASP B 529 " pdb=" NH2 ARG B 570 " model vdw 1.998 3.120 nonbonded pdb=" OH TYR B 272 " pdb=" OG SER B 330 " model vdw 2.200 3.040 nonbonded pdb=" O ASN B 618 " pdb=" C ASN B 619 " model vdw 2.251 3.270 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.254 3.040 nonbonded pdb=" NH1 ARG B 548 " pdb=" OE2 GLU B 613 " model vdw 2.260 3.120 ... (remaining 40422 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: 1.270 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.010 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 5155 Z= 0.405 Angle : 0.946 13.661 6991 Z= 0.644 Chirality : 0.053 0.375 758 Planarity : 0.006 0.076 869 Dihedral : 16.155 89.907 1840 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.02 % Favored : 93.48 % Rotamer: Outliers : 0.56 % Allowed : 19.66 % Favored : 79.78 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.37), residues: 598 helix: 2.56 (0.26), residues: 428 sheet: None (None), residues: 0 loop : -2.15 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 126 TYR 0.013 0.001 TYR B 148 PHE 0.029 0.002 PHE B 474 TRP 0.015 0.001 TRP B 514 HIS 0.005 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 5154) covalent geometry : angle 0.93611 ( 6989) SS BOND : bond 0.00782 ( 1) SS BOND : angle 8.08542 ( 2) hydrogen bonds : bond 0.16311 ( 355) hydrogen bonds : angle 5.42700 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.201 Fit side-chains REVERT: B 133 LEU cc_start: 0.8813 (tp) cc_final: 0.8587 (tp) REVERT: B 452 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7912 (tt0) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.0903 time to fit residues: 11.3157 Evaluate side-chains 65 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN B 310 ASN B 441 HIS B 479 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099999 restraints weight = 8137.166| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.50 r_work: 0.3120 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 5155 Z= 0.149 Angle : 0.610 10.121 6991 Z= 0.322 Chirality : 0.038 0.128 758 Planarity : 0.004 0.039 869 Dihedral : 5.340 59.086 666 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 3.37 % Allowed : 19.66 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.15 (0.36), residues: 598 helix: 2.67 (0.25), residues: 433 sheet: None (None), residues: 0 loop : -2.23 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 371 TYR 0.013 0.001 TYR B 352 PHE 0.017 0.001 PHE B 610 TRP 0.017 0.001 TRP B 514 HIS 0.018 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5154) covalent geometry : angle 0.60822 ( 6989) SS BOND : bond 0.00212 ( 1) SS BOND : angle 2.85243 ( 2) hydrogen bonds : bond 0.04541 ( 355) hydrogen bonds : angle 3.91451 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.118 Fit side-chains REVERT: B 133 LEU cc_start: 0.8415 (tp) cc_final: 0.8103 (tp) REVERT: B 215 MET cc_start: 0.8913 (mmm) cc_final: 0.8694 (mmm) REVERT: B 340 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8525 (t) REVERT: B 399 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8176 (mm-40) REVERT: B 472 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7668 (ttm110) REVERT: B 499 HIS cc_start: 0.9012 (m90) cc_final: 0.8417 (m90) outliers start: 18 outliers final: 5 residues processed: 79 average time/residue: 0.0771 time to fit residues: 7.7305 Evaluate side-chains 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 HIS B 479 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099374 restraints weight = 8081.819| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.50 r_work: 0.3099 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 5155 Z= 0.143 Angle : 0.575 9.736 6991 Z= 0.304 Chirality : 0.039 0.132 758 Planarity : 0.004 0.044 869 Dihedral : 4.339 30.787 661 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.35 % Favored : 94.48 % Rotamer: Outliers : 3.37 % Allowed : 19.66 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.24 (0.36), residues: 598 helix: 2.66 (0.25), residues: 439 sheet: None (None), residues: 0 loop : -2.14 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 82 TYR 0.012 0.001 TYR B 352 PHE 0.020 0.001 PHE B 610 TRP 0.014 0.001 TRP B 514 HIS 0.020 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5154) covalent geometry : angle 0.57338 ( 6989) SS BOND : bond 0.00267 ( 1) SS BOND : angle 2.40446 ( 2) hydrogen bonds : bond 0.04146 ( 355) hydrogen bonds : angle 3.79734 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: B 29 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8811 (tt) REVERT: B 411 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8596 (tm-30) REVERT: B 499 HIS cc_start: 0.9020 (m90) cc_final: 0.8338 (m90) REVERT: B 508 MET cc_start: 0.7424 (mmt) cc_final: 0.7130 (mmp) REVERT: B 514 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7774 (t-100) outliers start: 18 outliers final: 8 residues processed: 79 average time/residue: 0.0864 time to fit residues: 8.7003 Evaluate side-chains 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 514 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 620 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.0000 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 441 HIS ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.137877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.099709 restraints weight = 8080.785| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.52 r_work: 0.3113 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 5155 Z= 0.131 Angle : 0.559 9.826 6991 Z= 0.297 Chirality : 0.037 0.133 758 Planarity : 0.004 0.044 869 Dihedral : 4.274 30.867 661 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 2.81 % Allowed : 20.41 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.45 (0.36), residues: 598 helix: 2.82 (0.25), residues: 440 sheet: None (None), residues: 0 loop : -2.13 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.011 0.001 TYR B 73 PHE 0.025 0.001 PHE B 54 TRP 0.014 0.001 TRP B 395 HIS 0.021 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5154) covalent geometry : angle 0.55801 ( 6989) SS BOND : bond 0.00280 ( 1) SS BOND : angle 2.25062 ( 2) hydrogen bonds : bond 0.03836 ( 355) hydrogen bonds : angle 3.69814 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.204 Fit side-chains REVERT: B 29 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8785 (tt) REVERT: B 411 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 518 TYR cc_start: 0.7695 (t80) cc_final: 0.6706 (t80) REVERT: B 573 TRP cc_start: 0.8007 (p-90) cc_final: 0.7499 (p-90) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.0955 time to fit residues: 9.2561 Evaluate side-chains 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097826 restraints weight = 8131.919| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.53 r_work: 0.3125 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 5155 Z= 0.135 Angle : 0.567 9.624 6991 Z= 0.300 Chirality : 0.037 0.131 758 Planarity : 0.004 0.041 869 Dihedral : 4.256 30.530 661 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.85 % Favored : 93.98 % Rotamer: Outliers : 2.81 % Allowed : 21.35 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.58 (0.36), residues: 598 helix: 3.00 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -2.14 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 82 TYR 0.011 0.001 TYR B 73 PHE 0.019 0.001 PHE B 54 TRP 0.012 0.001 TRP B 395 HIS 0.027 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 5154) covalent geometry : angle 0.56610 ( 6989) SS BOND : bond 0.00270 ( 1) SS BOND : angle 2.24506 ( 2) hydrogen bonds : bond 0.03775 ( 355) hydrogen bonds : angle 3.67823 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.224 Fit side-chains REVERT: B 5 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7926 (mt-10) REVERT: B 29 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 411 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 508 MET cc_start: 0.7379 (mmt) cc_final: 0.7081 (mmp) REVERT: B 514 TRP cc_start: 0.8246 (OUTLIER) cc_final: 0.7482 (t-100) REVERT: B 518 TYR cc_start: 0.7711 (t80) cc_final: 0.6678 (t80) REVERT: B 573 TRP cc_start: 0.7706 (p-90) cc_final: 0.7328 (p-90) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.0931 time to fit residues: 8.5664 Evaluate side-chains 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 514 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 620 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 overall best weight: 0.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097118 restraints weight = 8298.344| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.56 r_work: 0.3113 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 5155 Z= 0.136 Angle : 0.554 9.474 6991 Z= 0.293 Chirality : 0.038 0.131 758 Planarity : 0.004 0.073 869 Dihedral : 4.259 30.850 661 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.52 % Favored : 94.31 % Rotamer: Outliers : 3.37 % Allowed : 21.54 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.58 (0.36), residues: 598 helix: 2.86 (0.25), residues: 443 sheet: None (None), residues: 0 loop : -1.96 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 82 TYR 0.012 0.001 TYR B 524 PHE 0.018 0.001 PHE B 610 TRP 0.016 0.001 TRP B 514 HIS 0.027 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5154) covalent geometry : angle 0.55300 ( 6989) SS BOND : bond 0.00250 ( 1) SS BOND : angle 2.19940 ( 2) hydrogen bonds : bond 0.03733 ( 355) hydrogen bonds : angle 3.66981 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.200 Fit side-chains REVERT: B 5 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7964 (mt-10) REVERT: B 29 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8796 (tt) REVERT: B 410 LEU cc_start: 0.8046 (tp) cc_final: 0.7629 (tt) REVERT: B 411 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8585 (tm-30) REVERT: B 489 MET cc_start: 0.8524 (tpp) cc_final: 0.7984 (ttt) REVERT: B 508 MET cc_start: 0.7360 (mmt) cc_final: 0.7054 (mmp) REVERT: B 514 TRP cc_start: 0.8213 (OUTLIER) cc_final: 0.7853 (t-100) REVERT: B 518 TYR cc_start: 0.7604 (t80) cc_final: 0.6621 (t80) REVERT: B 573 TRP cc_start: 0.7839 (p-90) cc_final: 0.7464 (p-90) outliers start: 18 outliers final: 12 residues processed: 72 average time/residue: 0.0849 time to fit residues: 7.8891 Evaluate side-chains 72 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 514 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 620 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 10 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: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** 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 = 0.3710 r_free = 0.3710 target = 0.132505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095252 restraints weight = 7958.096| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.25 r_work: 0.3029 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5155 Z= 0.144 Angle : 0.562 9.563 6991 Z= 0.297 Chirality : 0.038 0.131 758 Planarity : 0.004 0.077 869 Dihedral : 4.254 31.236 661 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.52 % Favored : 94.31 % Rotamer: Outliers : 3.37 % Allowed : 21.91 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.55 (0.36), residues: 598 helix: 2.82 (0.24), residues: 443 sheet: None (None), residues: 0 loop : -1.94 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 82 TYR 0.011 0.001 TYR B 73 PHE 0.018 0.001 PHE B 610 TRP 0.015 0.001 TRP B 514 HIS 0.006 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5154) covalent geometry : angle 0.56081 ( 6989) SS BOND : bond 0.00194 ( 1) SS BOND : angle 2.06353 ( 2) hydrogen bonds : bond 0.03804 ( 355) hydrogen bonds : angle 3.69853 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 29 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8817 (tt) REVERT: B 410 LEU cc_start: 0.8221 (tp) cc_final: 0.7816 (tt) REVERT: B 411 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8798 (tm-30) REVERT: B 489 MET cc_start: 0.8742 (tpp) cc_final: 0.8248 (ttt) REVERT: B 508 MET cc_start: 0.7439 (mmt) cc_final: 0.7121 (mmp) REVERT: B 514 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.8074 (t-100) outliers start: 18 outliers final: 13 residues processed: 70 average time/residue: 0.0768 time to fit residues: 7.0949 Evaluate side-chains 70 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 514 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 620 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097518 restraints weight = 8019.819| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.31 r_work: 0.3054 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 5155 Z= 0.122 Angle : 0.548 9.643 6991 Z= 0.290 Chirality : 0.037 0.131 758 Planarity : 0.004 0.080 869 Dihedral : 4.202 31.909 661 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.52 % Favored : 94.31 % Rotamer: Outliers : 3.00 % Allowed : 21.35 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.68 (0.36), residues: 598 helix: 2.87 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -1.77 (0.50), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.011 0.001 TYR B 73 PHE 0.017 0.001 PHE B 610 TRP 0.021 0.001 TRP B 573 HIS 0.009 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5154) covalent geometry : angle 0.54631 ( 6989) SS BOND : bond 0.00332 ( 1) SS BOND : angle 2.22003 ( 2) hydrogen bonds : bond 0.03608 ( 355) hydrogen bonds : angle 3.66549 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.217 Fit side-chains REVERT: B 5 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 29 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8828 (tt) REVERT: B 411 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8688 (tm-30) REVERT: B 489 MET cc_start: 0.8695 (tpp) cc_final: 0.8344 (ttt) REVERT: B 508 MET cc_start: 0.7360 (mmt) cc_final: 0.7035 (mmp) REVERT: B 514 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.8120 (t-100) REVERT: B 518 TYR cc_start: 0.7775 (t80) cc_final: 0.6949 (t80) outliers start: 16 outliers final: 11 residues processed: 71 average time/residue: 0.0805 time to fit residues: 7.5178 Evaluate side-chains 70 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 514 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 620 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095790 restraints weight = 7995.578| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.28 r_work: 0.3029 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5155 Z= 0.145 Angle : 0.557 9.534 6991 Z= 0.296 Chirality : 0.038 0.131 758 Planarity : 0.004 0.084 869 Dihedral : 4.240 30.601 661 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 3.56 % Allowed : 21.16 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.62 (0.36), residues: 598 helix: 2.85 (0.24), residues: 444 sheet: None (None), residues: 0 loop : -1.87 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.011 0.001 TYR B 352 PHE 0.018 0.001 PHE B 610 TRP 0.019 0.001 TRP B 573 HIS 0.007 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5154) covalent geometry : angle 0.55542 ( 6989) SS BOND : bond 0.00152 ( 1) SS BOND : angle 2.20871 ( 2) hydrogen bonds : bond 0.03783 ( 355) hydrogen bonds : angle 3.68439 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.199 Fit side-chains REVERT: B 5 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8266 (mt-10) REVERT: B 29 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8837 (tt) REVERT: B 410 LEU cc_start: 0.8332 (tp) cc_final: 0.7930 (tt) REVERT: B 411 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 489 MET cc_start: 0.8766 (tpp) cc_final: 0.8421 (ttt) REVERT: B 514 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.8051 (t-100) REVERT: B 518 TYR cc_start: 0.7771 (t80) cc_final: 0.6925 (t80) outliers start: 19 outliers final: 15 residues processed: 68 average time/residue: 0.0543 time to fit residues: 5.1272 Evaluate side-chains 71 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 514 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 620 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098589 restraints weight = 8007.820| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.25 r_work: 0.3066 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 5155 Z= 0.118 Angle : 0.536 9.638 6991 Z= 0.285 Chirality : 0.037 0.129 758 Planarity : 0.004 0.085 869 Dihedral : 4.168 31.282 661 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.85 % Favored : 93.98 % Rotamer: Outliers : 2.81 % Allowed : 21.91 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.73 (0.36), residues: 598 helix: 2.91 (0.24), residues: 445 sheet: None (None), residues: 0 loop : -1.79 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.010 0.001 TYR B 73 PHE 0.016 0.001 PHE B 610 TRP 0.016 0.001 TRP B 573 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5154) covalent geometry : angle 0.53453 ( 6989) SS BOND : bond 0.00236 ( 1) SS BOND : angle 2.23742 ( 2) hydrogen bonds : bond 0.03513 ( 355) hydrogen bonds : angle 3.66002 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.247 Fit side-chains REVERT: B 5 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 29 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8798 (tt) REVERT: B 411 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8640 (tm-30) REVERT: B 489 MET cc_start: 0.8704 (tpp) cc_final: 0.8397 (ttt) REVERT: B 514 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.7969 (t-100) REVERT: B 518 TYR cc_start: 0.7693 (t80) cc_final: 0.6911 (t80) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 0.0722 time to fit residues: 6.5647 Evaluate side-chains 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 443 TYR Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 514 TRP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 539 LYS Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 575 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096214 restraints weight = 8096.449| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.31 r_work: 0.3030 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5155 Z= 0.135 Angle : 0.546 9.613 6991 Z= 0.290 Chirality : 0.037 0.131 758 Planarity : 0.004 0.085 869 Dihedral : 4.194 31.423 661 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 2.81 % Allowed : 22.10 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: 2.68 (0.36), residues: 598 helix: 2.87 (0.24), residues: 446 sheet: None (None), residues: 0 loop : -1.82 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.011 0.001 TYR B 352 PHE 0.018 0.001 PHE B 610 TRP 0.016 0.001 TRP B 573 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5154) covalent geometry : angle 0.54484 ( 6989) SS BOND : bond 0.00165 ( 1) SS BOND : angle 2.20619 ( 2) hydrogen bonds : bond 0.03691 ( 355) hydrogen bonds : angle 3.67585 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.12 seconds wall clock time: 25 minutes 3.37 seconds (1503.37 seconds total)