Starting phenix.real_space_refine on Wed Jul 1 23:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktu_62566/07_2026/9ktu_62566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktu_62566/07_2026/9ktu_62566.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 { model { file = "/net/cci-nas-00/data/ceres_data/9ktu_62566/07_2026/9ktu_62566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktu_62566/07_2026/9ktu_62566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ktu_62566/07_2026/9ktu_62566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktu_62566/07_2026/9ktu_62566.map" } 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= 0.026 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: 6 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2823 2.51 5 N 634 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4212 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4199 Classifications: {'peptide': 529} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 501} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BAL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 5 Ad-hoc single atom residues: {' CL': 1, ' NA': 1} Classifications: {'water': 5} Link IDs: {None: 4} Chain breaks: 2 Time building chain proxies: 0.97, per 1000 atoms: 0.23 Number of scatterers: 4212 At special positions: 0 Unit cell: (76.38, 66.33, 87.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 32 16.00 Na 1 11.00 O 721 8.00 N 634 7.00 C 2823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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: 0.28 Conformation dependent library (CDL) restraints added in 126.2 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL A 701 " Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 79.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.514A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.625A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 117 removed outlier: 4.027A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 152 removed outlier: 3.697A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 219 through 236 Processing helix chain 'A' and resid 246 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.986A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.155A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.901A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.890A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.777A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.650A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.614A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.729A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 4.163A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.051A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.543A pdb=" N VAL A 471 " --> pdb=" O CYS A 467 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 474 " --> pdb=" O TRP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.637A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.007A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 277 hydrogen bonds defined for protein. 813 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: 0.68 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1221 1.34 - 1.46: 1188 1.46 - 1.58: 1887 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4342 Sorted by residual: bond pdb=" N GLU A 584 " pdb=" CA GLU A 584 " ideal model delta sigma weight residual 1.460 1.441 0.018 1.29e-02 6.01e+03 2.03e+00 bond pdb=" CA GLU A 584 " pdb=" C GLU A 584 " ideal model delta sigma weight residual 1.522 1.513 0.009 8.40e-03 1.42e+04 1.22e+00 bond pdb=" C GLU A 584 " pdb=" O GLU A 584 " ideal model delta sigma weight residual 1.248 1.235 0.013 1.26e-02 6.30e+03 1.08e+00 bond pdb=" C BAL A 701 " pdb=" O BAL A 701 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.31e-01 bond pdb=" CG PRO A 367 " pdb=" CD PRO A 367 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.03e-01 ... (remaining 4337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 5693 1.06 - 2.11: 173 2.11 - 3.17: 44 3.17 - 4.22: 7 4.22 - 5.28: 6 Bond angle restraints: 5923 Sorted by residual: angle pdb=" C BAL A 701 " pdb=" CA BAL A 701 " pdb=" CB BAL A 701 " ideal model delta sigma weight residual 110.50 114.55 -4.05 1.50e+00 4.44e-01 7.30e+00 angle pdb=" N BAL A 701 " pdb=" CB BAL A 701 " pdb=" CA BAL A 701 " ideal model delta sigma weight residual 110.40 113.62 -3.22 1.50e+00 4.44e-01 4.60e+00 angle pdb=" CA GLU A 584 " pdb=" C GLU A 584 " pdb=" O GLU A 584 " ideal model delta sigma weight residual 119.59 121.25 -1.66 7.80e-01 1.64e+00 4.50e+00 angle pdb=" CA GLU A 584 " pdb=" C GLU A 584 " pdb=" N PRO A 585 " ideal model delta sigma weight residual 119.06 116.98 2.08 1.05e+00 9.07e-01 3.91e+00 angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.84 122.30 -2.46 1.25e+00 6.40e-01 3.88e+00 ... (remaining 5918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 2287 15.33 - 30.66: 126 30.66 - 46.00: 25 46.00 - 61.33: 7 61.33 - 76.66: 1 Dihedral angle restraints: 2446 sinusoidal: 923 harmonic: 1523 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual 93.00 150.00 -57.00 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG A 575 " pdb=" CD ARG A 575 " pdb=" NE ARG A 575 " pdb=" CZ ARG A 575 " ideal model delta sinusoidal sigma weight residual -180.00 -137.49 -42.51 2 1.50e+01 4.44e-03 9.74e+00 ... (remaining 2443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 401 0.029 - 0.057: 166 0.057 - 0.086: 52 0.086 - 0.114: 30 0.114 - 0.143: 4 Chirality restraints: 653 Sorted by residual: chirality pdb=" CA PHE A 58 " pdb=" N PHE A 58 " pdb=" C PHE A 58 " pdb=" CB PHE A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA THR A 512 " pdb=" N THR A 512 " pdb=" C THR A 512 " pdb=" CB THR A 512 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" C PRO A 384 " pdb=" CB PRO A 384 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 650 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 129 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C VAL A 129 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 129 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 130 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 130 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" C ILE A 130 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE A 130 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 131 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 132 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C SER A 132 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 132 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 133 " 0.009 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 53 2.69 - 3.24: 4359 3.24 - 3.79: 6949 3.79 - 4.35: 9148 4.35 - 4.90: 15723 Nonbonded interactions: 36232 Sorted by model distance: nonbonded pdb=" CD1 LEU A 306 " pdb=" O HOH A 804 " model vdw 2.135 3.460 nonbonded pdb=" NH2 ARG A 41 " pdb=" OD2 ASP A 416 " model vdw 2.246 3.120 nonbonded pdb=" O GLY A 570 " pdb=" NE ARG A 575 " model vdw 2.253 3.120 nonbonded pdb=" OE1 GLN A 103 " pdb=" OG SER A 322 " model vdw 2.261 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.293 3.120 ... (remaining 36227 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: 4.850 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.003 0.023 4343 Z= 0.126 Angle : 0.493 5.281 5925 Z= 0.279 Chirality : 0.039 0.143 653 Planarity : 0.004 0.032 722 Dihedral : 10.346 76.659 1479 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.00 % Allowed : 4.01 % Favored : 93.99 % Cbeta Deviations : 0.21 % 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: 1.06 (0.37), residues: 523 helix: 1.36 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -0.84 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 575 TYR 0.013 0.001 TYR A 69 PHE 0.011 0.001 PHE A 276 TRP 0.008 0.001 TRP A 387 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 4342) covalent geometry : angle 0.49267 / 0.28 ( 5923) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 0.47834 / 0.26 ( 2) hydrogen bonds : bond 0.15676 / 9.90 ( 277) hydrogen bonds : angle 6.57107 / 4.57 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.092 Fit side-chains REVERT: A 211 ASP cc_start: 0.8143 (p0) cc_final: 0.7881 (p0) REVERT: A 247 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.4991 (m-80) REVERT: A 452 MET cc_start: 0.8441 (tpp) cc_final: 0.8005 (tpt) REVERT: A 532 TYR cc_start: 0.8681 (t80) cc_final: 0.8191 (t80) outliers start: 9 outliers final: 2 residues processed: 75 average time/residue: 0.0451 time to fit residues: 4.7623 Evaluate side-chains 59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 247 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.137717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.124907 restraints weight = 5056.986| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.53 r_work: 0.3219 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4343 Z= 0.149 Angle : 0.529 5.410 5925 Z= 0.278 Chirality : 0.040 0.138 653 Planarity : 0.004 0.034 722 Dihedral : 5.468 57.039 579 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.67 % Allowed : 7.57 % Favored : 89.76 % Cbeta Deviations : 0.21 % 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: 1.59 (0.38), residues: 523 helix: 1.77 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.89 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.019 0.001 TYR A 137 PHE 0.017 0.001 PHE A 338 TRP 0.019 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4342) covalent geometry : angle 0.52889 / 0.28 ( 5923) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 0.22890 / 0.13 ( 2) hydrogen bonds : bond 0.04489 / 2.83 ( 277) hydrogen bonds : angle 4.66349 / 3.22 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.147 Fit side-chains REVERT: A 176 MET cc_start: 0.7496 (tpp) cc_final: 0.6795 (mpp) REVERT: A 211 ASP cc_start: 0.8524 (p0) cc_final: 0.8307 (p0) REVERT: A 247 TYR cc_start: 0.5552 (OUTLIER) cc_final: 0.4693 (m-80) REVERT: A 331 CYS cc_start: 0.7812 (m) cc_final: 0.7602 (m) REVERT: A 344 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8012 (mt) REVERT: A 414 LEU cc_start: 0.7536 (mm) cc_final: 0.7254 (mt) REVERT: A 452 MET cc_start: 0.8547 (tpp) cc_final: 0.8158 (tpt) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.0419 time to fit residues: 4.3589 Evaluate side-chains 61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 0.0970 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.137756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.124751 restraints weight = 4961.167| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.53 r_work: 0.3217 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4343 Z= 0.136 Angle : 0.517 9.139 5925 Z= 0.270 Chirality : 0.039 0.140 653 Planarity : 0.004 0.039 722 Dihedral : 5.566 56.818 579 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.45 % Allowed : 10.47 % Favored : 87.08 % Cbeta Deviations : 0.21 % 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: 1.62 (0.37), residues: 523 helix: 1.79 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.87 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.016 0.001 TYR A 137 PHE 0.014 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4342) covalent geometry : angle 0.51430 / 0.27 ( 5923) SS BOND : bond 0.00708 / 0.37 ( 1) SS BOND : angle 2.96036 / 1.69 ( 2) hydrogen bonds : bond 0.04187 / 2.65 ( 277) hydrogen bonds : angle 4.49075 / 3.12 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.150 Fit side-chains REVERT: A 176 MET cc_start: 0.7377 (tpp) cc_final: 0.6606 (mpp) REVERT: A 211 ASP cc_start: 0.8532 (p0) cc_final: 0.8320 (p0) REVERT: A 344 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 414 LEU cc_start: 0.7503 (mm) cc_final: 0.7228 (mt) REVERT: A 452 MET cc_start: 0.8580 (tpp) cc_final: 0.8120 (tpt) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 0.0483 time to fit residues: 4.0384 Evaluate side-chains 59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.137993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125304 restraints weight = 4963.946| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.47 r_work: 0.3240 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4343 Z= 0.126 Angle : 0.493 6.788 5925 Z= 0.256 Chirality : 0.039 0.132 653 Planarity : 0.004 0.042 722 Dihedral : 5.476 58.176 577 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.67 % Allowed : 11.14 % Favored : 86.19 % Cbeta Deviations : 0.21 % 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: 1.67 (0.37), residues: 523 helix: 1.84 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.88 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.016 0.001 TYR A 137 PHE 0.014 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 4342) covalent geometry : angle 0.48880 / 0.25 ( 5923) SS BOND : bond 0.00395 / 0.21 ( 1) SS BOND : angle 3.59212 / 1.98 ( 2) hydrogen bonds : bond 0.03910 / 2.49 ( 277) hydrogen bonds : angle 4.34428 / 3.02 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.165 Fit side-chains REVERT: A 150 PHE cc_start: 0.8094 (m-10) cc_final: 0.7772 (m-80) REVERT: A 176 MET cc_start: 0.7379 (tpp) cc_final: 0.6694 (mpp) REVERT: A 211 ASP cc_start: 0.8541 (p0) cc_final: 0.8335 (p0) REVERT: A 247 TYR cc_start: 0.5474 (OUTLIER) cc_final: 0.4693 (m-80) REVERT: A 344 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8097 (mt) REVERT: A 414 LEU cc_start: 0.7556 (mm) cc_final: 0.7107 (mm) REVERT: A 452 MET cc_start: 0.8588 (tpp) cc_final: 0.8146 (tpt) outliers start: 12 outliers final: 7 residues processed: 63 average time/residue: 0.0435 time to fit residues: 3.9750 Evaluate side-chains 63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.0670 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.139464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126825 restraints weight = 4965.676| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.47 r_work: 0.3254 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4343 Z= 0.109 Angle : 0.469 6.000 5925 Z= 0.244 Chirality : 0.038 0.120 653 Planarity : 0.004 0.043 722 Dihedral : 5.112 56.776 577 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.67 % Allowed : 11.80 % Favored : 85.52 % Cbeta Deviations : 0.21 % 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: 1.80 (0.37), residues: 523 helix: 1.98 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.013 0.001 TYR A 138 PHE 0.011 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 4342) covalent geometry : angle 0.46590 / 0.24 ( 5923) SS BOND : bond 0.00387 / 0.20 ( 1) SS BOND : angle 2.78082 / 1.54 ( 2) hydrogen bonds : bond 0.03642 / 2.31 ( 277) hydrogen bonds : angle 4.20301 / 2.93 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.150 Fit side-chains REVERT: A 150 PHE cc_start: 0.8105 (m-10) cc_final: 0.7820 (m-80) REVERT: A 176 MET cc_start: 0.7321 (tpp) cc_final: 0.6575 (mpp) REVERT: A 247 TYR cc_start: 0.5466 (OUTLIER) cc_final: 0.4716 (m-80) REVERT: A 344 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 414 LEU cc_start: 0.7544 (mm) cc_final: 0.7085 (mm) REVERT: A 426 TYR cc_start: 0.5421 (OUTLIER) cc_final: 0.5155 (t80) REVERT: A 452 MET cc_start: 0.8543 (tpp) cc_final: 0.8063 (tpt) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.0442 time to fit residues: 3.9270 Evaluate side-chains 62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.0060 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.139427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.127219 restraints weight = 5036.352| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.41 r_work: 0.3256 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4343 Z= 0.111 Angle : 0.467 5.676 5925 Z= 0.243 Chirality : 0.038 0.121 653 Planarity : 0.004 0.044 722 Dihedral : 4.899 56.653 577 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.67 % Allowed : 12.25 % Favored : 85.08 % Cbeta Deviations : 0.21 % 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: 1.79 (0.38), residues: 523 helix: 1.98 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.03 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.013 0.001 TYR A 69 PHE 0.013 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4342) covalent geometry : angle 0.46439 / 0.24 ( 5923) SS BOND : bond 0.00288 / 0.15 ( 1) SS BOND : angle 2.59628 / 1.43 ( 2) hydrogen bonds : bond 0.03607 / 2.29 ( 277) hydrogen bonds : angle 4.15785 / 2.90 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.142 Fit side-chains REVERT: A 150 PHE cc_start: 0.8118 (m-10) cc_final: 0.7826 (m-80) REVERT: A 176 MET cc_start: 0.7296 (tpp) cc_final: 0.6609 (mpp) REVERT: A 247 TYR cc_start: 0.5450 (OUTLIER) cc_final: 0.4761 (m-80) REVERT: A 344 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8171 (mt) REVERT: A 359 ILE cc_start: 0.8451 (mt) cc_final: 0.8188 (mt) REVERT: A 414 LEU cc_start: 0.7609 (mm) cc_final: 0.7153 (mm) REVERT: A 452 MET cc_start: 0.8544 (tpp) cc_final: 0.8027 (tpt) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.0359 time to fit residues: 3.3245 Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 TYR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.138076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.125021 restraints weight = 5087.839| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.56 r_work: 0.3219 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4343 Z= 0.137 Angle : 0.487 5.734 5925 Z= 0.254 Chirality : 0.039 0.126 653 Planarity : 0.004 0.044 722 Dihedral : 4.917 56.589 577 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.90 % Allowed : 11.36 % Favored : 85.75 % Cbeta Deviations : 0.21 % 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: 1.71 (0.37), residues: 523 helix: 1.91 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.03 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.015 0.001 PHE A 79 TRP 0.010 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4342) covalent geometry : angle 0.48464 / 0.25 ( 5923) SS BOND : bond 0.00349 / 0.18 ( 1) SS BOND : angle 2.70804 / 1.48 ( 2) hydrogen bonds : bond 0.03785 / 2.41 ( 277) hydrogen bonds : angle 4.22542 / 2.94 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.091 Fit side-chains REVERT: A 150 PHE cc_start: 0.8119 (m-10) cc_final: 0.7830 (m-80) REVERT: A 176 MET cc_start: 0.7321 (tpp) cc_final: 0.6583 (mpp) REVERT: A 344 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8067 (mt) REVERT: A 359 ILE cc_start: 0.8411 (mt) cc_final: 0.8171 (mt) REVERT: A 414 LEU cc_start: 0.7525 (mm) cc_final: 0.7049 (mm) REVERT: A 426 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.5167 (t80) REVERT: A 452 MET cc_start: 0.8548 (tpp) cc_final: 0.8095 (tpt) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.0407 time to fit residues: 3.6107 Evaluate side-chains 64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 13 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.140078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127724 restraints weight = 5016.269| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.40 r_work: 0.3270 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4343 Z= 0.109 Angle : 0.468 5.475 5925 Z= 0.244 Chirality : 0.038 0.121 653 Planarity : 0.004 0.044 722 Dihedral : 4.783 56.267 577 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.90 % Allowed : 11.36 % Favored : 85.75 % Cbeta Deviations : 0.21 % 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: 1.79 (0.37), residues: 523 helix: 2.02 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.13 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.012 0.001 TYR A 69 PHE 0.012 0.001 PHE A 79 TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 4342) covalent geometry : angle 0.46545 / 0.24 ( 5923) SS BOND : bond 0.00287 / 0.15 ( 1) SS BOND : angle 2.61447 / 1.44 ( 2) hydrogen bonds : bond 0.03527 / 2.25 ( 277) hydrogen bonds : angle 4.13161 / 2.89 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.165 Fit side-chains REVERT: A 150 PHE cc_start: 0.8107 (m-10) cc_final: 0.7846 (m-80) REVERT: A 344 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8162 (mt) REVERT: A 359 ILE cc_start: 0.8425 (mt) cc_final: 0.8174 (mt) REVERT: A 452 MET cc_start: 0.8538 (tpp) cc_final: 0.8038 (tpt) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.0463 time to fit residues: 4.0853 Evaluate side-chains 62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.137330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124793 restraints weight = 5069.317| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.46 r_work: 0.3226 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4343 Z= 0.145 Angle : 0.508 5.847 5925 Z= 0.265 Chirality : 0.039 0.128 653 Planarity : 0.004 0.044 722 Dihedral : 4.901 56.344 577 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.90 % Allowed : 11.58 % Favored : 85.52 % Cbeta Deviations : 0.21 % 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: 1.68 (0.37), residues: 523 helix: 1.91 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.08 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 201 TYR 0.015 0.001 TYR A 69 PHE 0.017 0.001 PHE A 79 TRP 0.010 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4342) covalent geometry : angle 0.50605 / 0.26 ( 5923) SS BOND : bond 0.00355 / 0.19 ( 1) SS BOND : angle 2.74566 / 1.50 ( 2) hydrogen bonds : bond 0.03869 / 2.47 ( 277) hydrogen bonds : angle 4.25670 / 2.96 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.091 Fit side-chains REVERT: A 150 PHE cc_start: 0.8089 (m-10) cc_final: 0.7831 (m-80) REVERT: A 176 MET cc_start: 0.7348 (tpp) cc_final: 0.6779 (mpp) REVERT: A 344 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 359 ILE cc_start: 0.8445 (mt) cc_final: 0.8212 (mt) REVERT: A 452 MET cc_start: 0.8566 (tpp) cc_final: 0.8149 (tpt) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.0406 time to fit residues: 3.4369 Evaluate side-chains 63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.138171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.125533 restraints weight = 4959.991| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.47 r_work: 0.3231 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4343 Z= 0.128 Angle : 0.493 5.758 5925 Z= 0.258 Chirality : 0.039 0.125 653 Planarity : 0.004 0.044 722 Dihedral : 4.869 56.209 577 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.34 % Allowed : 11.36 % Favored : 85.30 % Cbeta Deviations : 0.21 % 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: 1.69 (0.37), residues: 523 helix: 1.92 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.10 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.011 0.001 TRP A 470 HIS 0.001 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4342) covalent geometry : angle 0.49105 / 0.26 ( 5923) SS BOND : bond 0.00362 / 0.19 ( 1) SS BOND : angle 2.69251 / 1.48 ( 2) hydrogen bonds : bond 0.03759 / 2.40 ( 277) hydrogen bonds : angle 4.21871 / 2.94 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.092 Fit side-chains REVERT: A 150 PHE cc_start: 0.8086 (m-10) cc_final: 0.7831 (m-80) REVERT: A 176 MET cc_start: 0.7319 (tpp) cc_final: 0.6733 (mpp) REVERT: A 344 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8087 (mt) REVERT: A 359 ILE cc_start: 0.8413 (mt) cc_final: 0.8163 (mt) REVERT: A 452 MET cc_start: 0.8543 (tpp) cc_final: 0.8084 (tpt) outliers start: 15 outliers final: 12 residues processed: 61 average time/residue: 0.0283 time to fit residues: 2.5845 Evaluate side-chains 64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 1 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.141144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.128621 restraints weight = 4997.299| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.43 r_work: 0.3273 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4343 Z= 0.106 Angle : 0.473 5.219 5925 Z= 0.246 Chirality : 0.038 0.119 653 Planarity : 0.004 0.044 722 Dihedral : 4.700 55.917 577 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.56 % Allowed : 11.14 % Favored : 85.30 % Cbeta Deviations : 0.21 % 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: 1.85 (0.37), residues: 523 helix: 2.08 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.21 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.012 0.001 TYR A 137 PHE 0.011 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 4342) covalent geometry : angle 0.47088 / 0.25 ( 5923) SS BOND : bond 0.00305 / 0.16 ( 1) SS BOND : angle 2.46773 / 1.37 ( 2) hydrogen bonds : bond 0.03398 / 2.17 ( 277) hydrogen bonds : angle 4.09123 / 2.86 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.54 seconds wall clock time: 19 minutes 8.97 seconds (1148.97 seconds total)