Starting phenix.real_space_refine on Fri Aug 22 17:14:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cff_45544/08_2025/9cff_45544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cff_45544/08_2025/9cff_45544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cff_45544/08_2025/9cff_45544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cff_45544/08_2025/9cff_45544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cff_45544/08_2025/9cff_45544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cff_45544/08_2025/9cff_45544.map" } resolution = 3.0 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2077 2.51 5 N 554 2.21 5 O 619 1.98 5 H 3134 0.53 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6398 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1748 Classifications: {'peptide': 115} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "L" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1653 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2997 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Time building chain proxies: 1.44, per 1000 atoms: 0.23 Number of scatterers: 6398 At special positions: 0 Unit cell: (64.74, 91.3, 88.81, 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 14 16.00 O 619 8.00 N 554 7.00 C 2077 6.00 H 3134 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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: 0.54 Conformation dependent library (CDL) restraints added in 245.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 13.2% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.566A pdb=" N ASN H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.322A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.252A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.756A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.970A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR L 98 " --> pdb=" O ARG L 91 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP L 93 " --> pdb=" O ARG L 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR L 86 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.107A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.107A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 129 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3134 1.03 - 1.23: 73 1.23 - 1.43: 1406 1.43 - 1.62: 1856 1.62 - 1.82: 16 Bond restraints: 6485 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N GLU H 1 " pdb=" H2 GLU H 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" CG PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 6.94e+00 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 11641 4.61 - 9.21: 5 9.21 - 13.82: 2 13.82 - 18.43: 1 18.43 - 23.03: 1 Bond angle restraints: 11650 Sorted by residual: angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 109.47 86.44 23.03 3.00e+00 1.11e-01 5.89e+01 angle pdb=" N PRO A 479 " pdb=" CD PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 103.20 92.94 10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.74e+01 angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 109.47 124.83 -15.36 3.00e+00 1.11e-01 2.62e+01 angle pdb=" CA PRO A 479 " pdb=" CB PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 104.50 95.47 9.03 1.90e+00 2.77e-01 2.26e+01 ... (remaining 11645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2780 17.88 - 35.76: 231 35.76 - 53.64: 79 53.64 - 71.51: 28 71.51 - 89.39: 7 Dihedral angle restraints: 3125 sinusoidal: 1665 harmonic: 1460 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -159.50 73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CA CYS A 480 " pdb=" C CYS A 480 " pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual 79.00 12.21 66.79 1 2.00e+01 2.50e-03 1.45e+01 ... (remaining 3122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 233 0.027 - 0.053: 178 0.053 - 0.080: 30 0.080 - 0.106: 20 0.106 - 0.133: 25 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE H 92 " pdb=" N ILE H 92 " pdb=" C ILE H 92 " pdb=" CB ILE H 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 483 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 384 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 521 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " -0.027 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 479 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " -0.022 5.00e-02 4.00e+02 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 607 2.22 - 2.82: 13455 2.82 - 3.41: 16672 3.41 - 4.01: 24164 4.01 - 4.60: 36247 Nonbonded interactions: 91145 Sorted by model distance: nonbonded pdb="HH22 ARG A 454 " pdb=" O SER A 469 " model vdw 1.625 2.450 nonbonded pdb="HH11 ARG H 97 " pdb=" OD2 ASP H 104 " model vdw 1.629 2.450 nonbonded pdb="HH22 ARG H 97 " pdb=" OD1 ASN A 487 " model vdw 1.630 2.450 nonbonded pdb=" HG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 1.644 2.450 nonbonded pdb=" O TRP A 353 " pdb="HH21 ARG A 466 " model vdw 1.657 2.450 ... (remaining 91140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.070 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: 0.040 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 3357 Z= 0.157 Angle : 0.626 11.425 4570 Z= 0.327 Chirality : 0.045 0.133 486 Planarity : 0.005 0.050 595 Dihedral : 15.883 89.393 1204 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 16.06 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.53 (0.42), residues: 411 helix: -3.43 (0.74), residues: 33 sheet: 0.33 (0.48), residues: 127 loop : -0.19 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 509 TYR 0.011 0.001 TYR H 33 PHE 0.008 0.001 PHE A 429 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3351) covalent geometry : angle 0.62475 ( 4558) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.04858 ( 12) hydrogen bonds : bond 0.22414 ( 113) hydrogen bonds : angle 10.75876 ( 300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 1.4656 time to fit residues: 79.3665 Evaluate side-chains 31 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain A residue 339 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.043655 restraints weight = 29389.731| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.13 r_work: 0.2574 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3357 Z= 0.170 Angle : 0.596 7.121 4570 Z= 0.304 Chirality : 0.045 0.129 486 Planarity : 0.005 0.052 595 Dihedral : 5.954 57.293 469 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 3.10 % Allowed : 18.03 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.38 (0.42), residues: 411 helix: -3.36 (0.71), residues: 33 sheet: 0.52 (0.47), residues: 124 loop : -0.14 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.009 0.001 TYR H 33 PHE 0.006 0.001 PHE L 83 TRP 0.006 0.001 TRP H 105 HIS 0.002 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3351) covalent geometry : angle 0.59490 ( 4558) SS BOND : bond 0.00331 ( 6) SS BOND : angle 1.02981 ( 12) hydrogen bonds : bond 0.03656 ( 113) hydrogen bonds : angle 6.81281 ( 300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLU cc_start: 0.4156 (tt0) cc_final: 0.3885 (tt0) REVERT: A 390 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8100 (mp) REVERT: A 516 GLU cc_start: 0.8138 (tt0) cc_final: 0.7868 (tt0) outliers start: 11 outliers final: 3 residues processed: 41 average time/residue: 1.2410 time to fit residues: 52.4384 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.043813 restraints weight = 29943.444| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.12 r_work: 0.2591 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3357 Z= 0.113 Angle : 0.543 5.080 4570 Z= 0.276 Chirality : 0.044 0.130 486 Planarity : 0.004 0.036 595 Dihedral : 5.334 56.616 465 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.92 % Favored : 96.84 % Rotamer: Outliers : 1.69 % Allowed : 20.00 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.24 (0.42), residues: 411 helix: -3.10 (0.75), residues: 33 sheet: 0.79 (0.49), residues: 114 loop : -0.13 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.005 0.001 TYR H 33 PHE 0.004 0.001 PHE A 497 TRP 0.005 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3351) covalent geometry : angle 0.54227 ( 4558) SS BOND : bond 0.00265 ( 6) SS BOND : angle 0.71326 ( 12) hydrogen bonds : bond 0.02996 ( 113) hydrogen bonds : angle 6.15937 ( 300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8505 (m) REVERT: L 106 GLU cc_start: 0.3967 (tt0) cc_final: 0.3690 (tp30) REVERT: A 390 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 516 GLU cc_start: 0.8348 (tt0) cc_final: 0.8052 (tt0) REVERT: A 519 HIS cc_start: 0.8040 (m90) cc_final: 0.7787 (t70) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 1.2905 time to fit residues: 46.5160 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.042774 restraints weight = 30081.497| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.15 r_work: 0.2567 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3357 Z= 0.167 Angle : 0.546 4.579 4570 Z= 0.277 Chirality : 0.044 0.127 486 Planarity : 0.004 0.051 595 Dihedral : 5.335 55.194 465 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 2.54 % Allowed : 18.87 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.18 (0.43), residues: 411 helix: -2.85 (0.89), residues: 27 sheet: 0.63 (0.45), residues: 129 loop : -0.15 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.010 0.001 TYR H 33 PHE 0.005 0.001 PHE A 429 TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3351) covalent geometry : angle 0.54494 ( 4558) SS BOND : bond 0.00316 ( 6) SS BOND : angle 0.85339 ( 12) hydrogen bonds : bond 0.02872 ( 113) hydrogen bonds : angle 5.78318 ( 300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8531 (m) REVERT: H 13 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8621 (mp10) REVERT: L 106 GLU cc_start: 0.4153 (tt0) cc_final: 0.3765 (tp30) REVERT: A 390 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 519 HIS cc_start: 0.8068 (m90) cc_final: 0.7805 (t70) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 1.2500 time to fit residues: 50.2439 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.052469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.043150 restraints weight = 30460.093| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.18 r_work: 0.2580 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3357 Z= 0.131 Angle : 0.531 4.755 4570 Z= 0.270 Chirality : 0.043 0.126 486 Planarity : 0.004 0.045 595 Dihedral : 5.407 52.761 465 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.11 % Rotamer: Outliers : 1.69 % Allowed : 20.56 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.13 (0.43), residues: 411 helix: -2.51 (0.98), residues: 27 sheet: 0.64 (0.45), residues: 129 loop : -0.13 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.007 0.001 TYR H 33 PHE 0.004 0.001 PHE A 429 TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3351) covalent geometry : angle 0.53076 ( 4558) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.67024 ( 12) hydrogen bonds : bond 0.02640 ( 113) hydrogen bonds : angle 5.56010 ( 300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8529 (m) REVERT: H 13 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8674 (mp10) REVERT: H 26 GLU cc_start: 0.7874 (pm20) cc_final: 0.7455 (pm20) REVERT: L 106 GLU cc_start: 0.4076 (tt0) cc_final: 0.3543 (tp30) REVERT: A 519 HIS cc_start: 0.8043 (m90) cc_final: 0.7713 (t70) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 1.3044 time to fit residues: 46.9878 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.043782 restraints weight = 30563.918| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.12 r_work: 0.2645 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3357 Z= 0.124 Angle : 0.525 4.495 4570 Z= 0.267 Chirality : 0.043 0.125 486 Planarity : 0.004 0.051 595 Dihedral : 5.280 52.198 465 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 20.28 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.04 (0.43), residues: 411 helix: -2.43 (0.96), residues: 27 sheet: 0.73 (0.45), residues: 129 loop : -0.09 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.019 0.001 TYR A 369 PHE 0.003 0.001 PHE A 429 TRP 0.005 0.001 TRP A 436 HIS 0.003 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3351) covalent geometry : angle 0.52488 ( 4558) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.64229 ( 12) hydrogen bonds : bond 0.02554 ( 113) hydrogen bonds : angle 5.40929 ( 300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8405 (m) REVERT: H 13 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8652 (mp10) REVERT: H 26 GLU cc_start: 0.7810 (pm20) cc_final: 0.7383 (pm20) REVERT: L 106 GLU cc_start: 0.3897 (tt0) cc_final: 0.3400 (tp30) REVERT: A 519 HIS cc_start: 0.8142 (m90) cc_final: 0.7685 (t70) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 1.1273 time to fit residues: 45.5196 Evaluate side-chains 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.042978 restraints weight = 30651.594| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.10 r_work: 0.2619 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3357 Z= 0.170 Angle : 0.547 5.521 4570 Z= 0.278 Chirality : 0.044 0.125 486 Planarity : 0.004 0.054 595 Dihedral : 5.411 53.054 465 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.13 % Rotamer: Outliers : 2.54 % Allowed : 19.72 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.16 (0.42), residues: 411 helix: -2.42 (0.97), residues: 27 sheet: 0.65 (0.44), residues: 129 loop : -0.19 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.008 0.001 TYR H 33 PHE 0.005 0.001 PHE A 429 TRP 0.004 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 3351) covalent geometry : angle 0.54609 ( 4558) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.76213 ( 12) hydrogen bonds : bond 0.02653 ( 113) hydrogen bonds : angle 5.45321 ( 300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8430 (m) REVERT: H 13 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8664 (mp10) REVERT: H 26 GLU cc_start: 0.7847 (pm20) cc_final: 0.7444 (pm20) REVERT: L 106 GLU cc_start: 0.3912 (tt0) cc_final: 0.3407 (tp30) REVERT: A 519 HIS cc_start: 0.8155 (m90) cc_final: 0.7717 (t-170) outliers start: 9 outliers final: 4 residues processed: 37 average time/residue: 1.2284 time to fit residues: 46.8977 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.043754 restraints weight = 30207.449| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.06 r_work: 0.2638 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3357 Z= 0.116 Angle : 0.533 5.758 4570 Z= 0.272 Chirality : 0.043 0.127 486 Planarity : 0.004 0.057 595 Dihedral : 5.248 52.690 465 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 20.56 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.12 (0.42), residues: 411 helix: -2.43 (0.95), residues: 27 sheet: 0.73 (0.45), residues: 129 loop : -0.18 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.006 0.001 TYR A 369 PHE 0.005 0.001 PHE A 342 TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3351) covalent geometry : angle 0.53312 ( 4558) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.58217 ( 12) hydrogen bonds : bond 0.02459 ( 113) hydrogen bonds : angle 5.33838 ( 300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8435 (m) REVERT: H 13 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8699 (mp10) REVERT: H 26 GLU cc_start: 0.7841 (pm20) cc_final: 0.7435 (pm20) REVERT: L 106 GLU cc_start: 0.3834 (tt0) cc_final: 0.3325 (tp30) REVERT: A 519 HIS cc_start: 0.8114 (m90) cc_final: 0.7670 (t70) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 1.3010 time to fit residues: 49.5558 Evaluate side-chains 32 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.0000 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.044409 restraints weight = 30784.461| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.09 r_work: 0.2689 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 3357 Z= 0.096 Angle : 0.536 6.599 4570 Z= 0.273 Chirality : 0.043 0.127 486 Planarity : 0.004 0.058 595 Dihedral : 4.968 51.536 465 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 1.13 % Allowed : 21.69 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.04 (0.42), residues: 411 helix: -2.37 (0.88), residues: 33 sheet: 1.03 (0.47), residues: 118 loop : -0.17 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.018 0.001 TYR A 369 PHE 0.004 0.001 PHE A 497 TRP 0.005 0.001 TRP H 105 HIS 0.002 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3351) covalent geometry : angle 0.53580 ( 4558) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.49195 ( 12) hydrogen bonds : bond 0.02309 ( 113) hydrogen bonds : angle 5.12448 ( 300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8404 (m) REVERT: H 13 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8704 (mp10) REVERT: H 26 GLU cc_start: 0.7799 (pm20) cc_final: 0.7475 (pm20) REVERT: L 106 GLU cc_start: 0.3902 (tt0) cc_final: 0.3314 (tp30) REVERT: A 519 HIS cc_start: 0.8099 (m90) cc_final: 0.7581 (t70) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 1.2632 time to fit residues: 48.2546 Evaluate side-chains 32 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.043903 restraints weight = 30645.752| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.07 r_work: 0.2671 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3357 Z= 0.143 Angle : 0.552 6.515 4570 Z= 0.279 Chirality : 0.044 0.140 486 Planarity : 0.004 0.061 595 Dihedral : 4.086 24.398 463 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.13 % Rotamer: Outliers : 1.13 % Allowed : 22.82 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.14 (0.42), residues: 411 helix: -2.33 (0.95), residues: 29 sheet: 0.84 (0.47), residues: 120 loop : -0.23 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 357 TYR 0.008 0.001 TYR A 369 PHE 0.004 0.001 PHE A 429 TRP 0.004 0.001 TRP H 105 HIS 0.005 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3351) covalent geometry : angle 0.55202 ( 4558) SS BOND : bond 0.00289 ( 6) SS BOND : angle 0.68131 ( 12) hydrogen bonds : bond 0.02474 ( 113) hydrogen bonds : angle 5.15785 ( 300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 32 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8391 (m) REVERT: H 13 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8676 (mp10) REVERT: H 26 GLU cc_start: 0.7836 (pm20) cc_final: 0.7489 (pm20) REVERT: L 106 GLU cc_start: 0.3982 (tt0) cc_final: 0.3377 (tp30) REVERT: A 519 HIS cc_start: 0.8156 (m90) cc_final: 0.7655 (t70) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 1.3701 time to fit residues: 45.1331 Evaluate side-chains 32 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043381 restraints weight = 30759.124| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.08 r_work: 0.2633 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3357 Z= 0.153 Angle : 0.553 6.481 4570 Z= 0.281 Chirality : 0.044 0.123 486 Planarity : 0.004 0.062 595 Dihedral : 4.239 29.146 463 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.11 % Favored : 94.65 % Rotamer: Outliers : 1.13 % Allowed : 22.82 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -0.15 (0.42), residues: 411 helix: -2.38 (0.94), residues: 29 sheet: 0.73 (0.45), residues: 127 loop : -0.20 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 357 TYR 0.015 0.001 TYR A 369 PHE 0.004 0.001 PHE A 429 TRP 0.005 0.001 TRP H 105 HIS 0.008 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3351) covalent geometry : angle 0.55238 ( 4558) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.71954 ( 12) hydrogen bonds : bond 0.02526 ( 113) hydrogen bonds : angle 5.26316 ( 300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.66 seconds wall clock time: 43 minutes 23.26 seconds (2603.26 seconds total)